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authorBonfaceKilz2020-08-26 19:12:33 +0300
committerBonfaceKilz2020-08-26 19:12:33 +0300
commit303e4b71c2172da5be19c84d4be5a062329ac013 (patch)
tree130496e7b4c6fe2157c14abd50be941823ed40b9
parent7717f0d3d4802d115a8b5ace4d379864ba5b1188 (diff)
downloadgenenetwork2-303e4b71c2172da5be19c84d4be5a062329ac013.tar.gz
Remove "from __future__ import new_feature" statements
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-future>
-rw-r--r--test/requests/link_checker.py1
-rw-r--r--test/requests/main_web_functionality.py22
-rw-r--r--test/requests/mapping_tests.py1
-rw-r--r--test/requests/navigation_tests.py1
-rwxr-xr-xtest/requests/test-website.py2
-rw-r--r--webtests/browser_run.py4
-rw-r--r--webtests/correlation_matrix_test.py2
-rw-r--r--webtests/correlation_test.py2
-rw-r--r--webtests/marker_regression_test.py2
-rw-r--r--webtests/show_trait_js_test.py2
-rw-r--r--webtests/test_runner.py4
-rw-r--r--wqflask/base/data_set.py1
-rw-r--r--wqflask/base/mrna_assay_tissue_data.py4
-rw-r--r--wqflask/base/species.py4
-rw-r--r--wqflask/base/trait.py2
-rw-r--r--wqflask/maintenance/convert_dryad_to_bimbam.py3
-rw-r--r--wqflask/maintenance/convert_geno_to_bimbam.py3
-rw-r--r--wqflask/maintenance/gen_select_dataset.py10
-rw-r--r--wqflask/maintenance/generate_kinship_from_bimbam.py3
-rw-r--r--wqflask/maintenance/generate_probesetfreeze_file.py2
-rw-r--r--wqflask/maintenance/geno_to_json.py3
-rw-r--r--wqflask/maintenance/get_group_samplelists.py2
-rw-r--r--wqflask/maintenance/print_benchmark.py4
-rw-r--r--wqflask/maintenance/quantile_normalize.py7
-rw-r--r--wqflask/maintenance/set_resource_defaults.py4
-rw-r--r--wqflask/utility/Plot.py2
-rw-r--r--wqflask/utility/after.py4
-rw-r--r--wqflask/utility/authentication_tools.py2
-rw-r--r--wqflask/utility/benchmark.py2
-rw-r--r--wqflask/utility/chunks.py2
-rw-r--r--wqflask/utility/db_tools.py2
-rw-r--r--wqflask/utility/gen_geno_ob.py4
-rw-r--r--wqflask/utility/genofile_parser.py1
-rw-r--r--wqflask/utility/helper_functions.py2
-rw-r--r--wqflask/utility/hmac.py4
-rw-r--r--wqflask/utility/redis_tools.py4
-rw-r--r--wqflask/utility/temp_data.py1
-rw-r--r--wqflask/wqflask/__init__.py2
-rw-r--r--wqflask/wqflask/api/correlation.py4
-rw-r--r--wqflask/wqflask/api/gen_menu.py2
-rw-r--r--wqflask/wqflask/api/mapping.py2
-rw-r--r--wqflask/wqflask/api/router.py4
-rw-r--r--wqflask/wqflask/collect.py3
-rw-r--r--wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py1
-rw-r--r--wqflask/wqflask/correlation/corr_scatter_plot.py4
-rw-r--r--wqflask/wqflask/correlation/correlation_functions.py4
-rw-r--r--wqflask/wqflask/correlation/show_corr_results.py2
-rw-r--r--wqflask/wqflask/correlation_matrix/show_corr_matrix.py2
-rw-r--r--wqflask/wqflask/do_search.py2
-rw-r--r--wqflask/wqflask/docs.py4
-rw-r--r--wqflask/wqflask/export_traits.py4
-rw-r--r--wqflask/wqflask/external_tools/send_to_bnw.py4
-rw-r--r--wqflask/wqflask/external_tools/send_to_geneweaver.py4
-rw-r--r--wqflask/wqflask/external_tools/send_to_webgestalt.py4
-rw-r--r--wqflask/wqflask/group_manager.py5
-rw-r--r--wqflask/wqflask/gsearch.py2
-rw-r--r--wqflask/wqflask/heatmap/heatmap.py2
-rw-r--r--wqflask/wqflask/interval_analyst/GeneUtil.py2
-rw-r--r--wqflask/wqflask/marker_regression/run_mapping.py4
-rw-r--r--wqflask/wqflask/model.py4
-rw-r--r--wqflask/wqflask/network_graph/network_graph.py2
-rw-r--r--wqflask/wqflask/news.py1
-rw-r--r--wqflask/wqflask/parser.py2
-rw-r--r--wqflask/wqflask/resource_manager.py4
-rw-r--r--wqflask/wqflask/search_results.py2
-rw-r--r--wqflask/wqflask/send_mail.py2
-rw-r--r--wqflask/wqflask/show_trait/SampleList.py2
-rw-r--r--wqflask/wqflask/show_trait/export_trait_data.py4
-rw-r--r--wqflask/wqflask/show_trait/show_trait.py2
-rw-r--r--wqflask/wqflask/snp_browser/snp_browser.py2
-rw-r--r--wqflask/wqflask/submit_bnw.py4
-rw-r--r--wqflask/wqflask/update_search_results.py2
-rw-r--r--wqflask/wqflask/user_login.py4
-rw-r--r--wqflask/wqflask/user_manager.py2
-rw-r--r--wqflask/wqflask/user_session.py2
-rw-r--r--wqflask/wqflask/views.py2
76 files changed, 45 insertions, 190 deletions
diff --git a/test/requests/link_checker.py b/test/requests/link_checker.py
index 5e16a5cd..949a33c8 100644
--- a/test/requests/link_checker.py
+++ b/test/requests/link_checker.py
@@ -1,4 +1,3 @@
-from __future__ import print_function
import re
import requests
from lxml.html import parse
diff --git a/test/requests/main_web_functionality.py b/test/requests/main_web_functionality.py
index d070dab9..78030307 100644
--- a/test/requests/main_web_functionality.py
+++ b/test/requests/main_web_functionality.py
@@ -1,9 +1,7 @@
-from __future__ import print_function
-import re
import requests
from lxml.html import parse
from link_checker import check_page
-from requests.exceptions import ConnectionError
+
def check_home(url):
doc = parse(url).getroot()
@@ -11,20 +9,23 @@ def check_home(url):
assert(search_button[0].value == "Search")
print("OK")
+
def check_search_page(host):
data = dict(
- species="mouse"
- , group="BXD"
- , type="Hippocampus mRNA"
- , dataset="HC_M2_0606_P"
- , search_terms_or=""
- , search_terms_and="MEAN=(15 16) LRS=(23 46)")
+ species="mouse",
+ group="BXD",
+ type="Hippocampus mRNA",
+ dataset="HC_M2_0606_P",
+ search_terms_or="",
+ search_terms_and="MEAN=(15 16) LRS=(23 46)")
result = requests.get(host+"/search", params=data)
found = result.text.find("records are shown below")
assert(found >= 0)
assert(result.status_code == 200)
print("OK")
- check_traits_page(host, "/show_trait?trait_id=1435395_s_at&dataset=HC_M2_0606_P")
+ check_traits_page(host, ("/show_trait?trait_id=1435395_"
+ "s_at&dataset=HC_M2_0606_P"))
+
def check_traits_page(host, traits_url):
doc = parse(host+traits_url).getroot()
@@ -33,6 +34,7 @@ def check_traits_page(host, traits_url):
print("OK")
check_page(host, host+traits_url)
+
def check_main_web_functionality(args_obj, parser):
print("")
print("Checking main web functionality...")
diff --git a/test/requests/mapping_tests.py b/test/requests/mapping_tests.py
index 5748a2a3..19b22c21 100644
--- a/test/requests/mapping_tests.py
+++ b/test/requests/mapping_tests.py
@@ -1,4 +1,3 @@
-from __future__ import print_function
import re
import copy
import json
diff --git a/test/requests/navigation_tests.py b/test/requests/navigation_tests.py
index eda27324..6b91c1fd 100644
--- a/test/requests/navigation_tests.py
+++ b/test/requests/navigation_tests.py
@@ -1,4 +1,3 @@
-from __future__ import print_function
import re
import requests
from lxml.html import parse
diff --git a/test/requests/test-website.py b/test/requests/test-website.py
index f90d1843..8bfb47c2 100755
--- a/test/requests/test-website.py
+++ b/test/requests/test-website.py
@@ -3,7 +3,7 @@
# env GN2_PROFILE=/home/wrk/opt/gn-latest ./bin/genenetwork2 ./etc/default_settings.py -c ../test/requests/test-website.py http://localhost:5003
#
# Mostly to pick up the Guix GN2_PROFILE and python modules
-from __future__ import print_function
+
import argparse
from link_checker import check_links
from link_checker import check_packaged_js_files
diff --git a/webtests/browser_run.py b/webtests/browser_run.py
index 2ec299c5..7ee540b7 100644
--- a/webtests/browser_run.py
+++ b/webtests/browser_run.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, division, print_function
-
__all__ = ('sleep', 'testmod', 'test')
from doctest import testmod
@@ -71,4 +69,4 @@ class Test(object):
-test = Test() \ No newline at end of file
+test = Test()
diff --git a/webtests/correlation_matrix_test.py b/webtests/correlation_matrix_test.py
index 8529c265..97114890 100644
--- a/webtests/correlation_matrix_test.py
+++ b/webtests/correlation_matrix_test.py
@@ -65,8 +65,6 @@ text: 0.608\n71
"""
-from __future__ import absolute_import, division, print_function
-
from browser_run import *
testmod()
diff --git a/webtests/correlation_test.py b/webtests/correlation_test.py
index aad3a69f..311bb847 100644
--- a/webtests/correlation_test.py
+++ b/webtests/correlation_test.py
@@ -44,8 +44,6 @@ text: 1.000
"""
-from __future__ import absolute_import, division, print_function
-
from browser_run import *
testmod()
diff --git a/webtests/marker_regression_test.py b/webtests/marker_regression_test.py
index c4f76f53..9b4a4acb 100644
--- a/webtests/marker_regression_test.py
+++ b/webtests/marker_regression_test.py
@@ -48,8 +48,6 @@ text: 11.511
"""
-from __future__ import absolute_import, division, print_function
-
from browser_run import *
testmod()
diff --git a/webtests/show_trait_js_test.py b/webtests/show_trait_js_test.py
index 0fd2c16c..34ffd3b7 100644
--- a/webtests/show_trait_js_test.py
+++ b/webtests/show_trait_js_test.py
@@ -35,8 +35,6 @@ style: display: none;
"""
-from __future__ import absolute_import, division, print_function
-
from browser_run import *
testmod()
diff --git a/webtests/test_runner.py b/webtests/test_runner.py
index ef6d0d69..b5b590a6 100644
--- a/webtests/test_runner.py
+++ b/webtests/test_runner.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, division, print_function
-
import unittest
import doctest
import glob
@@ -25,4 +23,4 @@ def main():
runner.run(suite)
if __name__ == '__main__':
- main() \ No newline at end of file
+ main()
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 39a8a2ed..8ac7a279 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -18,7 +18,6 @@
#
# 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
diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py
index 6fec5dcd..33ce12bd 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
@@ -92,4 +90,4 @@ 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..e3f1bc4a 100644
--- a/wqflask/base/species.py
+++ b/wqflask/base/species.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, print_function, division
-
import collections
from flask import Flask, g
@@ -59,4 +57,4 @@ 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 09c41fa7..b20efd2a 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, division, print_function
-
import os
import string
import resource
diff --git a/wqflask/maintenance/convert_dryad_to_bimbam.py b/wqflask/maintenance/convert_dryad_to_bimbam.py
index e833b395..12ce35e9 100644
--- a/wqflask/maintenance/convert_dryad_to_bimbam.py
+++ b/wqflask/maintenance/convert_dryad_to_bimbam.py
@@ -6,7 +6,6 @@ Convert data dryad files to a BIMBAM _geno and _snps file
"""
-from __future__ import print_function, division, absolute_import
import sys
sys.path.append("..")
@@ -67,4 +66,4 @@ def convert_dryad_to_bimbam(filename):
if __name__=="__main__":
input_filename = "/home/zas1024/cfw_data/" + sys.argv[1] + ".txt"
- convert_dryad_to_bimbam(input_filename) \ No newline at end of file
+ convert_dryad_to_bimbam(input_filename)
diff --git a/wqflask/maintenance/convert_geno_to_bimbam.py b/wqflask/maintenance/convert_geno_to_bimbam.py
index 528b98cf..d49742f2 100644
--- a/wqflask/maintenance/convert_geno_to_bimbam.py
+++ b/wqflask/maintenance/convert_geno_to_bimbam.py
@@ -9,7 +9,6 @@ code
"""
-from __future__ import print_function, division, absolute_import
import sys
sys.path.append("..")
import os
@@ -187,4 +186,4 @@ if __name__=="__main__":
#convertob = ConvertGenoFile("/home/zas1024/gene/genotype_files/genotypes/SRxSHRSPF2.geno", "/home/zas1024/gene/genotype_files/new_genotypes/SRxSHRSPF2.json")
#convertob.convert()
ConvertGenoFile.process_all(Old_Geno_Directory, New_Geno_Directory)
- #ConvertGenoFiles(Geno_Directory) \ No newline at end of file
+ #ConvertGenoFiles(Geno_Directory)
diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py
index fd65a52a..544e2fd1 100644
--- a/wqflask/maintenance/gen_select_dataset.py
+++ b/wqflask/maintenance/gen_select_dataset.py
@@ -30,14 +30,6 @@ It needs to be run manually when database has been changed. Run it as
#
# This module is used by GeneNetwork project (www.genenetwork.org)
-from __future__ import print_function, division
-
-#from flask import config
-#
-#cdict = {}
-#config = config.Config(cdict).from_envvar('WQFLASK_SETTINGS')
-#print("cdict is:", cdict)
-
import sys
# NEW: Note we prepend the current path - otherwise a guix instance of GN2 may be used instead
@@ -319,4 +311,4 @@ def _test_it():
if __name__ == '__main__':
Conn = MySQLdb.Connect(**parse_db_uri())
Cursor = Conn.cursor()
- main() \ No newline at end of file
+ main()
diff --git a/wqflask/maintenance/generate_kinship_from_bimbam.py b/wqflask/maintenance/generate_kinship_from_bimbam.py
index b53f5dda..60257b28 100644
--- a/wqflask/maintenance/generate_kinship_from_bimbam.py
+++ b/wqflask/maintenance/generate_kinship_from_bimbam.py
@@ -8,7 +8,6 @@ and uses GEMMA to generate their corresponding kinship/relatedness matrix file
"""
-from __future__ import print_function, division, absolute_import
import sys
sys.path.append("..")
import os
@@ -58,4 +57,4 @@ if __name__=="__main__":
Bimbam_Directory = """/export/local/home/zas1024/genotype_files/genotype/bimbam/"""
GenerateKinshipMatrices.process_all(Geno_Directory, Bimbam_Directory)
- #./gemma -g /home/zas1024/genotype_files/genotype/bimbam/BXD_geno.txt -p /home/zas1024/genotype_files/genotype/bimbam/BXD_pheno.txt -gk 1 -o BXD \ No newline at end of file
+ #./gemma -g /home/zas1024/genotype_files/genotype/bimbam/BXD_geno.txt -p /home/zas1024/genotype_files/genotype/bimbam/BXD_pheno.txt -gk 1 -o BXD
diff --git a/wqflask/maintenance/generate_probesetfreeze_file.py b/wqflask/maintenance/generate_probesetfreeze_file.py
index 4231cc7c..b1e41e9a 100644
--- a/wqflask/maintenance/generate_probesetfreeze_file.py
+++ b/wqflask/maintenance/generate_probesetfreeze_file.py
@@ -1,7 +1,5 @@
#!/usr/bin/python
-from __future__ import absolute_import, print_function, division
-
import sys
# sys.path.insert(0, "..") - why?
diff --git a/wqflask/maintenance/geno_to_json.py b/wqflask/maintenance/geno_to_json.py
index 9579812a..7e7fd241 100644
--- a/wqflask/maintenance/geno_to_json.py
+++ b/wqflask/maintenance/geno_to_json.py
@@ -9,7 +9,6 @@ code
"""
-from __future__ import print_function, division, absolute_import
import sys
sys.path.append("..")
import os
@@ -194,4 +193,4 @@ if __name__=="__main__":
ConvertGenoFile.process_all(Old_Geno_Directory, New_Geno_Directory)
#ConvertGenoFiles(Geno_Directory)
- #process_csv(Input_File, Output_File) \ No newline at end of file
+ #process_csv(Input_File, Output_File)
diff --git a/wqflask/maintenance/get_group_samplelists.py b/wqflask/maintenance/get_group_samplelists.py
index fb22898a..3f9d0278 100644
--- a/wqflask/maintenance/get_group_samplelists.py
+++ b/wqflask/maintenance/get_group_samplelists.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, print_function, division
-
import os
import glob
import gzip
diff --git a/wqflask/maintenance/print_benchmark.py b/wqflask/maintenance/print_benchmark.py
index ae327cf3..b24ce4f1 100644
--- a/wqflask/maintenance/print_benchmark.py
+++ b/wqflask/maintenance/print_benchmark.py
@@ -1,7 +1,5 @@
#!/usr/bin/python
-from __future__ import absolute_import, print_function, division
-
import time
from pprint import pformat as pf
@@ -40,4 +38,4 @@ def new_main():
print(pf(TheCounter.Counters))
if __name__ == '__main__':
- new_main() \ No newline at end of file
+ new_main()
diff --git a/wqflask/maintenance/quantile_normalize.py b/wqflask/maintenance/quantile_normalize.py
index 4d6e03bf..701b2b50 100644
--- a/wqflask/maintenance/quantile_normalize.py
+++ b/wqflask/maintenance/quantile_normalize.py
@@ -1,10 +1,5 @@
-from __future__ import absolute_import, print_function, division
-
import sys
sys.path.insert(0, './')
-
-
-
import MySQLdb
import urllib.parse
@@ -126,4 +121,4 @@ if __name__ == '__main__':
}
)
- print(response) \ No newline at end of file
+ print(response)
diff --git a/wqflask/maintenance/set_resource_defaults.py b/wqflask/maintenance/set_resource_defaults.py
index abd5416c..4177c124 100644
--- a/wqflask/maintenance/set_resource_defaults.py
+++ b/wqflask/maintenance/set_resource_defaults.py
@@ -16,8 +16,6 @@ To run:
"""
-from __future__ import print_function, division
-
import sys
import json
@@ -163,4 +161,4 @@ def main():
if __name__ == '__main__':
Conn = MySQLdb.Connect(**parse_db_uri())
Cursor = Conn.cursor()
- main() \ No newline at end of file
+ main()
diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py
index 48a5c7ba..61f408d2 100644
--- a/wqflask/utility/Plot.py
+++ b/wqflask/utility/Plot.py
@@ -24,8 +24,6 @@
#
# Last updated by GeneNetwork Core Team 2010/10/20
-from __future__ import print_function
-
from PIL import ImageColor
from PIL import ImageDraw
from PIL import ImageFont
diff --git a/wqflask/utility/after.py b/wqflask/utility/after.py
index b628a0a4..06091ecb 100644
--- a/wqflask/utility/after.py
+++ b/wqflask/utility/after.py
@@ -1,5 +1,3 @@
-from __future__ import print_function, division, absolute_import
-
"""
See: http://flask.pocoo.org/docs/patterns/deferredcallbacks/#deferred-callbacks
@@ -13,4 +11,4 @@ def after_this_request(f):
if not hasattr(g, 'after_request_callbacks'):
g.after_request_callbacks = []
g.after_request_callbacks.append(f)
- return f \ No newline at end of file
+ return f
diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py
index bc03eb55..0e499180 100644
--- a/wqflask/utility/authentication_tools.py
+++ b/wqflask/utility/authentication_tools.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, print_function, division
-
import json
import requests
diff --git a/wqflask/utility/benchmark.py b/wqflask/utility/benchmark.py
index 221e5151..ea5a0ab6 100644
--- a/wqflask/utility/benchmark.py
+++ b/wqflask/utility/benchmark.py
@@ -1,5 +1,3 @@
-from __future__ import print_function, division, absolute_import
-
import collections
import inspect
import time
diff --git a/wqflask/utility/chunks.py b/wqflask/utility/chunks.py
index d91b9bf4..9a7db102 100644
--- a/wqflask/utility/chunks.py
+++ b/wqflask/utility/chunks.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, print_function, division
-
import math
import time
diff --git a/wqflask/utility/db_tools.py b/wqflask/utility/db_tools.py
index 4034f39c..92bde505 100644
--- a/wqflask/utility/db_tools.py
+++ b/wqflask/utility/db_tools.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, print_function, division
-
from MySQLdb import escape_string as escape
def create_in_clause(items):
diff --git a/wqflask/utility/gen_geno_ob.py b/wqflask/utility/gen_geno_ob.py
index ae42f834..81085ffe 100644
--- a/wqflask/utility/gen_geno_ob.py
+++ b/wqflask/utility/gen_geno_ob.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, division, print_function
-
import utility.logger
logger = utility.logger.getLogger(__name__ )
@@ -178,4 +176,4 @@ class Locus(object):
if allele in list(geno_table.keys()):
self.genotype.append(geno_table[allele])
else: #ZS: Some genotype appears that isn't specified in the metadata, make it unknown
- self.genotype.append("U") \ No newline at end of file
+ self.genotype.append("U")
diff --git a/wqflask/utility/genofile_parser.py b/wqflask/utility/genofile_parser.py
index af306731..0b736176 100644
--- a/wqflask/utility/genofile_parser.py
+++ b/wqflask/utility/genofile_parser.py
@@ -1,7 +1,6 @@
# CTL analysis for GN2
# Author / Maintainer: Danny Arends <Danny.Arends@gmail.com>
-from __future__ import print_function, division, absolute_import
import sys
import os
import glob
diff --git a/wqflask/utility/helper_functions.py b/wqflask/utility/helper_functions.py
index 107c9ec6..7eb7f013 100644
--- a/wqflask/utility/helper_functions.py
+++ b/wqflask/utility/helper_functions.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, print_function, division
-
from base import data_set
from base.trait import create_trait
from base.species import TheSpecies
diff --git a/wqflask/utility/hmac.py b/wqflask/utility/hmac.py
index b08be97e..73e28790 100644
--- a/wqflask/utility/hmac.py
+++ b/wqflask/utility/hmac.py
@@ -1,5 +1,3 @@
-from __future__ import print_function, division, absolute_import
-
import hmac
import hashlib
@@ -37,4 +35,4 @@ def url_for_hmac(endpoint, **values):
return url + combiner + "hm=" + hm
app.jinja_env.globals.update(url_for_hmac=url_for_hmac,
- data_hmac=data_hmac) \ No newline at end of file
+ data_hmac=data_hmac)
diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py
index 1377a564..13ac5cfe 100644
--- a/wqflask/utility/redis_tools.py
+++ b/wqflask/utility/redis_tools.py
@@ -1,5 +1,3 @@
-from __future__ import print_function, division, absolute_import
-
import uuid
import simplejson as json
import datetime
@@ -306,4 +304,4 @@ def change_resource_owner(resource_id, new_owner_id):
the_resource['owner_id'] = new_owner_id
Redis.delete("resource")
- Redis.hset("resources", resource_id, json.dumps(the_resource)) \ No newline at end of file
+ Redis.hset("resources", resource_id, json.dumps(the_resource))
diff --git a/wqflask/utility/temp_data.py b/wqflask/utility/temp_data.py
index 2f2726c6..4144ae00 100644
--- a/wqflask/utility/temp_data.py
+++ b/wqflask/utility/temp_data.py
@@ -1,4 +1,3 @@
-from __future__ import print_function, division, absolute_import
from redis import Redis
import simplejson as json
diff --git a/wqflask/wqflask/__init__.py b/wqflask/wqflask/__init__.py
index d729aef5..e73f833f 100644
--- a/wqflask/wqflask/__init__.py
+++ b/wqflask/wqflask/__init__.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, division, print_function
-
import sys
import jinja2
diff --git a/wqflask/wqflask/api/correlation.py b/wqflask/wqflask/api/correlation.py
index eb05645e..7da13121 100644
--- a/wqflask/wqflask/api/correlation.py
+++ b/wqflask/wqflask/api/correlation.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, division, print_function
-
import collections
import scipy
@@ -234,4 +232,4 @@ def init_corr_params(start_vars):
'return_count' : return_count
}
- return corr_params \ No newline at end of file
+ return corr_params
diff --git a/wqflask/wqflask/api/gen_menu.py b/wqflask/wqflask/api/gen_menu.py
index 41966f78..1dcafe1f 100644
--- a/wqflask/wqflask/api/gen_menu.py
+++ b/wqflask/wqflask/api/gen_menu.py
@@ -1,5 +1,3 @@
-from __future__ import print_function, division
-
from flask import g
diff --git a/wqflask/wqflask/api/mapping.py b/wqflask/wqflask/api/mapping.py
index 92c27c9b..d59a69df 100644
--- a/wqflask/wqflask/api/mapping.py
+++ b/wqflask/wqflask/api/mapping.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, division, print_function
-
import string
from base import data_set
diff --git a/wqflask/wqflask/api/router.py b/wqflask/wqflask/api/router.py
index 5f9b81b8..acf7ce4a 100644
--- a/wqflask/wqflask/api/router.py
+++ b/wqflask/wqflask/api/router.py
@@ -1,7 +1,5 @@
# GN2 API
-from __future__ import absolute_import, division, print_function
-
import os, io, csv, json, datetime, requests, yaml
import zlib
from zipfile import ZipFile, ZIP_DEFLATED
@@ -966,4 +964,4 @@ def get_group_id(group_name):
if group_id:
return group_id[0]
else:
- return None \ No newline at end of file
+ return None
diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py
index 06c00930..15383603 100644
--- a/wqflask/wqflask/collect.py
+++ b/wqflask/wqflask/collect.py
@@ -1,6 +1,3 @@
-from __future__ import print_function, division, absolute_import
-
-
import os
import hashlib
import datetime
diff --git a/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py b/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py
index 16832621..92de6073 100644
--- a/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py
+++ b/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py
@@ -18,7 +18,6 @@
#
# This module is used by GeneNetwork project (www.genenetwork.org)
-from __future__ import absolute_import, print_function, division
from pprint import pformat as pf
from base.trait import create_trait
diff --git a/wqflask/wqflask/correlation/corr_scatter_plot.py b/wqflask/wqflask/correlation/corr_scatter_plot.py
index 57a8d85f..929cd2c9 100644
--- a/wqflask/wqflask/correlation/corr_scatter_plot.py
+++ b/wqflask/wqflask/correlation/corr_scatter_plot.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, print_function, division
-
import math
from flask import g
@@ -130,4 +128,4 @@ def get_intercept_coords(slope, intercept, x_range, y_range):
intercept_coords.append([x1, y1])
intercept_coords.append([x2, y2])
- return intercept_coords \ No newline at end of file
+ return intercept_coords
diff --git a/wqflask/wqflask/correlation/correlation_functions.py b/wqflask/wqflask/correlation/correlation_functions.py
index abaa212f..b883e361 100644
--- a/wqflask/wqflask/correlation/correlation_functions.py
+++ b/wqflask/wqflask/correlation/correlation_functions.py
@@ -24,8 +24,6 @@
#
# Last updated by NL 2011/03/23
-from __future__ import absolute_import, print_function, division
-
import math
import rpy2.robjects
import string
@@ -114,4 +112,4 @@ def get_trait_symbol_and_tissue_values(symbol_list=None):
tissue_data = MrnaAssayTissueData(gene_symbols=symbol_list)
if len(tissue_data.gene_symbols):
- return tissue_data.get_symbol_values_pairs() \ No newline at end of file
+ return tissue_data.get_symbol_values_pairs()
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 5ced30b6..e5b87c6a 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -18,8 +18,6 @@
#
# This module is used by GeneNetwork project (www.genenetwork.org)
-from __future__ import absolute_import, print_function, division
-
import collections
import json
import scipy
diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
index bd5aca1f..7b4bda31 100644
--- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
+++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
@@ -18,8 +18,6 @@
#
# This module is used by GeneNetwork project (www.genenetwork.org)
-from __future__ import absolute_import, print_function, division
-
import datetime
import math
import numpy as np
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index cc9c1860..de8e1e78 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -1,5 +1,3 @@
-from __future__ import print_function, division
-
import string
import requests
import json
diff --git a/wqflask/wqflask/docs.py b/wqflask/wqflask/docs.py
index 78407e22..8628b81d 100644
--- a/wqflask/wqflask/docs.py
+++ b/wqflask/wqflask/docs.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, print_function, division
-
import codecs
from flask import g
@@ -42,4 +40,4 @@ def update_text(start_vars):
sql = "UPDATE Docs SET content='{0}' WHERE entry='{1}';".format(content, start_vars['entry_type'])
g.db.execute(sql)
except:
- pass \ No newline at end of file
+ pass
diff --git a/wqflask/wqflask/export_traits.py b/wqflask/wqflask/export_traits.py
index 2f4e9aac..3a886537 100644
--- a/wqflask/wqflask/export_traits.py
+++ b/wqflask/wqflask/export_traits.py
@@ -1,5 +1,3 @@
-from __future__ import print_function, division
-
import csv
import xlsxwriter
import io
@@ -140,4 +138,4 @@ def sort_traits_by_group(trait_list=[]):
traits_by_group[trait.dataset.group.name].append(trait)
- return traits_by_group \ No newline at end of file
+ return traits_by_group
diff --git a/wqflask/wqflask/external_tools/send_to_bnw.py b/wqflask/wqflask/external_tools/send_to_bnw.py
index 68efd10d..efa17f05 100644
--- a/wqflask/wqflask/external_tools/send_to_bnw.py
+++ b/wqflask/wqflask/external_tools/send_to_bnw.py
@@ -18,8 +18,6 @@
#
# This module is used by GeneNetwork project (www.genenetwork.org)
-from __future__ import absolute_import, print_function, division
-
from base.trait import GeneralTrait
from utility import helper_functions, corr_result_helpers
@@ -69,4 +67,4 @@ class SendToBNW(object):
if has_none:
continue
self.form_value += ",".join(str(cell) for cell in row)
- self.form_value += ";" \ No newline at end of file
+ self.form_value += ";"
diff --git a/wqflask/wqflask/external_tools/send_to_geneweaver.py b/wqflask/wqflask/external_tools/send_to_geneweaver.py
index 9844bab4..93164233 100644
--- a/wqflask/wqflask/external_tools/send_to_geneweaver.py
+++ b/wqflask/wqflask/external_tools/send_to_geneweaver.py
@@ -18,8 +18,6 @@
#
# This module is used by GeneNetwork project (www.genenetwork.org)
-from __future__ import absolute_import, print_function, division
-
import string
from flask import Flask, g
@@ -109,4 +107,4 @@ def test_chip(trait_list):
chip_name = '%s_NA' % result[0]
return chip_name
- return chip_name \ No newline at end of file
+ return chip_name
diff --git a/wqflask/wqflask/external_tools/send_to_webgestalt.py b/wqflask/wqflask/external_tools/send_to_webgestalt.py
index 30ca024f..b255ba95 100644
--- a/wqflask/wqflask/external_tools/send_to_webgestalt.py
+++ b/wqflask/wqflask/external_tools/send_to_webgestalt.py
@@ -18,8 +18,6 @@
#
# This module is used by GeneNetwork project (www.genenetwork.org)
-from __future__ import absolute_import, print_function, division
-
import string
from flask import Flask, g
@@ -123,4 +121,4 @@ def gen_gene_id_list(trait_list):
trait_name_list.append(trait.name)
retrieve_trait_info(trait, trait.dataset)
gene_id_list.append(str(trait.geneid))
- return trait_name_list, gene_id_list \ No newline at end of file
+ return trait_name_list, gene_id_list
diff --git a/wqflask/wqflask/group_manager.py b/wqflask/wqflask/group_manager.py
index 24848ed8..e6079c3e 100644
--- a/wqflask/wqflask/group_manager.py
+++ b/wqflask/wqflask/group_manager.py
@@ -1,6 +1,3 @@
-
-from __future__ import print_function, division, absolute_import
-
from flask import (Flask, g, render_template, url_for, request, make_response,
redirect, flash)
@@ -142,4 +139,4 @@ def send_group_invites(group_id, user_email_list = [], user_type="members"):
else:
send_verification_email(user_details, template_name = "email/group_verification.txt", key_prefix = "verification_code", subject = "You've been invited to join a GeneNetwork user group")
-#@app.route() \ No newline at end of file
+#@app.route()
diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py
index c65a1415..6d797a29 100644
--- a/wqflask/wqflask/gsearch.py
+++ b/wqflask/wqflask/gsearch.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, print_function, division
-
import json
from flask import Flask, g
diff --git a/wqflask/wqflask/heatmap/heatmap.py b/wqflask/wqflask/heatmap/heatmap.py
index 1f1cdb90..cca5a4fc 100644
--- a/wqflask/wqflask/heatmap/heatmap.py
+++ b/wqflask/wqflask/heatmap/heatmap.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, print_function, division
-
import string
import os
import random
diff --git a/wqflask/wqflask/interval_analyst/GeneUtil.py b/wqflask/wqflask/interval_analyst/GeneUtil.py
index a39e5d0f..17c8ccbf 100644
--- a/wqflask/wqflask/interval_analyst/GeneUtil.py
+++ b/wqflask/wqflask/interval_analyst/GeneUtil.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, print_function, division
-
import string
from flask import Flask, g
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index 67512bc6..7ae84b16 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, print_function, division
-
from base.trait import GeneralTrait
from base import data_set #import create_dataset
@@ -711,4 +709,4 @@ def get_perm_strata(this_trait, sample_list, categorical_vars, used_samples):
list_to_numbers = [d[x] for x in perm_strata_strings]
perm_strata = list_to_numbers
- return perm_strata \ No newline at end of file
+ return perm_strata
diff --git a/wqflask/wqflask/model.py b/wqflask/wqflask/model.py
index a135761c..772f74e4 100644
--- a/wqflask/wqflask/model.py
+++ b/wqflask/wqflask/model.py
@@ -1,5 +1,3 @@
-from __future__ import print_function, division, absolute_import
-
import uuid
import datetime
@@ -168,4 +166,4 @@ def display_collapsible(number):
def user_uuid():
"""Unique cookie for a user"""
- user_uuid = request.cookies.get('user_uuid') \ No newline at end of file
+ user_uuid = request.cookies.get('user_uuid')
diff --git a/wqflask/wqflask/network_graph/network_graph.py b/wqflask/wqflask/network_graph/network_graph.py
index 2a4c4a93..70e5dd58 100644
--- a/wqflask/wqflask/network_graph/network_graph.py
+++ b/wqflask/wqflask/network_graph/network_graph.py
@@ -18,8 +18,6 @@
#
# This module is used by GeneNetwork project (www.genenetwork.org)
-from __future__ import absolute_import, print_function, division
-
import scipy
import simplejson as json
from pprint import pformat as pf
diff --git a/wqflask/wqflask/news.py b/wqflask/wqflask/news.py
index 20319756..0675ec4b 100644
--- a/wqflask/wqflask/news.py
+++ b/wqflask/wqflask/news.py
@@ -1,4 +1,3 @@
-from __future__ import absolute_import, print_function, division
from flask import g
class News(object):
diff --git a/wqflask/wqflask/parser.py b/wqflask/wqflask/parser.py
index 1ca5ecff..472dd30e 100644
--- a/wqflask/wqflask/parser.py
+++ b/wqflask/wqflask/parser.py
@@ -17,8 +17,6 @@ be acceptable.]
"""
-from __future__ import print_function, division
-
import re
from pprint import pformat as pf
diff --git a/wqflask/wqflask/resource_manager.py b/wqflask/wqflask/resource_manager.py
index 6b3e00fb..e883d5da 100644
--- a/wqflask/wqflask/resource_manager.py
+++ b/wqflask/wqflask/resource_manager.py
@@ -1,5 +1,3 @@
-from __future__ import print_function, division, absolute_import
-
import json
from flask import (Flask, g, render_template, url_for, request, make_response,
@@ -131,4 +129,4 @@ def get_group_names(group_masks):
this_mask['name'] = group_name
group_masks_with_names[group_id] = this_mask
- return group_masks_with_names \ No newline at end of file
+ return group_masks_with_names
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index c07a7670..f6c677a8 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, print_function, division
-
import re
import uuid
from math import *
diff --git a/wqflask/wqflask/send_mail.py b/wqflask/wqflask/send_mail.py
index bf5d0dd8..86e8a558 100644
--- a/wqflask/wqflask/send_mail.py
+++ b/wqflask/wqflask/send_mail.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, division, print_function
-
import datetime
import time
diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index f17e825e..6fcf7cec 100644
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, print_function, division
-
from flask import Flask, g
from base import webqtlCaseData
diff --git a/wqflask/wqflask/show_trait/export_trait_data.py b/wqflask/wqflask/show_trait/export_trait_data.py
index 68c3ad7d..2d76b935 100644
--- a/wqflask/wqflask/show_trait/export_trait_data.py
+++ b/wqflask/wqflask/show_trait/export_trait_data.py
@@ -1,5 +1,3 @@
-from __future__ import print_function, division
-
import simplejson as json
from pprint import pformat as pf
@@ -71,4 +69,4 @@ def cmp_samples(a, b):
else:
return 1
else:
- return -1 \ No newline at end of file
+ return -1
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 6a74cada..e93b0289 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, print_function, division
-
import string
import os
import datetime
diff --git a/wqflask/wqflask/snp_browser/snp_browser.py b/wqflask/wqflask/snp_browser/snp_browser.py
index b3d26caf..0db7e1fe 100644
--- a/wqflask/wqflask/snp_browser/snp_browser.py
+++ b/wqflask/wqflask/snp_browser/snp_browser.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, print_function, division
-
from flask import Flask, g, url_for
import string
diff --git a/wqflask/wqflask/submit_bnw.py b/wqflask/wqflask/submit_bnw.py
index 59e60dfd..a0e84c8c 100644
--- a/wqflask/wqflask/submit_bnw.py
+++ b/wqflask/wqflask/submit_bnw.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, print_function, division
-
from base.trait import GeneralTrait
from base import data_set
from utility import helper_functions
@@ -8,4 +6,4 @@ import utility.logger
logger = utility.logger.getLogger(__name__ )
def get_bnw_input(start_vars):
- logger.debug("BNW VARS:", start_vars) \ No newline at end of file
+ logger.debug("BNW VARS:", start_vars)
diff --git a/wqflask/wqflask/update_search_results.py b/wqflask/wqflask/update_search_results.py
index 68bea9d6..672f95b1 100644
--- a/wqflask/wqflask/update_search_results.py
+++ b/wqflask/wqflask/update_search_results.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, print_function, division
-
import json
from flask import Flask, g
diff --git a/wqflask/wqflask/user_login.py b/wqflask/wqflask/user_login.py
index 04672b45..10cb7319 100644
--- a/wqflask/wqflask/user_login.py
+++ b/wqflask/wqflask/user_login.py
@@ -1,5 +1,3 @@
-from __future__ import print_function, division, absolute_import
-
import os
import hashlib
import datetime
@@ -470,4 +468,4 @@ def register():
@app.errorhandler(401)
def unauthorized(error):
- return redirect(url_for('login')) \ No newline at end of file
+ return redirect(url_for('login'))
diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py
index 3c41e2b8..24191a15 100644
--- a/wqflask/wqflask/user_manager.py
+++ b/wqflask/wqflask/user_manager.py
@@ -1,5 +1,3 @@
-from __future__ import print_function, division, absolute_import
-
import os
import hashlib
import datetime
diff --git a/wqflask/wqflask/user_session.py b/wqflask/wqflask/user_session.py
index 71c31c57..c1f38396 100644
--- a/wqflask/wqflask/user_session.py
+++ b/wqflask/wqflask/user_session.py
@@ -1,5 +1,3 @@
-from __future__ import print_function, division, absolute_import
-
import datetime
import time
import uuid
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 83d5202e..b0489e64 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -2,8 +2,6 @@
#
# Main routing table for GN2
-from __future__ import absolute_import, division, print_function
-
import traceback # for error page
import os # for error gifs
import random # for random error gif