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Make some files compatible with Python3

Also enlarge the set of files tested with flake8 under Python3
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nsoranzo committed Jun 3, 2016
1 parent 30fd1d6 commit b93d31129840146a65abef954879136fb884b4c9
@@ -1,5 +1,19 @@
lib/galaxy/util/
lib/galaxy/jobs/runners/util/
contrib/
cron/
lib/galaxy/actions/
lib/galaxy/auth/
lib/galaxy/config.py
lib/galaxy/dependencies/
lib/galaxy/eggs/
lib/galaxy/exceptions/
lib/galaxy/external_services/
lib/galaxy/forms/
lib/galaxy/jobs/
lib/galaxy/objectstore/
lib/galaxy/openid/
lib/galaxy/quota/
lib/galaxy/sample_tracking/
lib/galaxy/tags/
lib/galaxy/tools/cwl/
lib/galaxy/tools/parser/
lib/galaxy/tools/lint.py
@@ -10,8 +24,40 @@ lib/galaxy/tools/linters/
lib/galaxy/tools/deps/
lib/galaxy/tools/toolbox/
lib/galaxy/tools/parser/
lib/galaxy/jobs/metrics/
lib/galaxy/objectstore/
lib/galaxy/tours/
lib/galaxy/util/
lib/galaxy/work/
lib/galaxy_ext/
lib/galaxy_utils/
lib/log_tempfile.py
lib/psyco_full.py
lib/pulsar/
lib/tool_shed/capsule/
lib/tool_shed/dependencies/
lib/tool_shed/grids/
lib/tool_shed/managers/
lib/tool_shed/metadata/
lib/tool_shed/repository_types/
lib/tool_shed/scripts/
lib/tool_shed/tools/
lib/tool_shed/util/
lib/tool_shed/utility_containers/
scripts/api/common.py
scripts/api/display.py
scripts/api/workflow_execute_parameters.py
scripts/auth/
scripts/cleanup_datasets/admin_cleanup_datasets.py
scripts/cleanup_datasets/cleanup_datasets.py
test/api/test_workflows_from_yaml.py
test/base/
test/casperjs/
test/functional/
test/integration/
test/manual/
test/unit/tools/test_actions.py
test/unit/workflows/test_run_parameters.py
tool_list.py
tools/data_source/
tools/evolution/
tools/sr_mapping/
tools/visualization/
@@ -23,11 +23,14 @@
Script for merging specific local Galaxy config galaxy.ini.cri with default Galaxy galaxy.ini.sample
'''
import ConfigParser
from __future__ import print_function

import logging
import optparse
import sys

from six.moves import configparser


def main():
# logging configuration
@@ -42,15 +45,15 @@ def main():

for option in ['sample', 'config']:
if getattr(options, option) is None:
print "Please supply a --%s parameter.\n" % (option)
print("Please supply a --%s parameter.\n" % (option))
parser.print_help()
sys.exit()

config_sample = ConfigParser.RawConfigParser()
config_sample = configparser.RawConfigParser()
config_sample.read(options.sample)
config_sample_content = open(options.sample, 'r').read()

config = ConfigParser.RawConfigParser()
config = configparser.RawConfigParser()
config.read(options.config)

logging.info("Merging your own config file %s into the sample one %s." % (options.config, options.sample))
@@ -3,6 +3,7 @@
check_galaxy can be run by hand, although it is meant to run from cron
via the check_galaxy.sh script in Galaxy's cron/ directory.
"""
from __future__ import print_function

import filecmp
import formatter
@@ -63,7 +64,7 @@ def usage():
try:
opts, args = getopt.getopt( sys.argv[1:], 'n' )
except getopt.GetoptError as e:
print str(e)
print(str(e))
usage()
if len( args ) < 1:
usage()
@@ -75,15 +76,15 @@ def usage():
for o, a in opts:
if o == "-n":
if debug:
print "Specified -n, will create a new history"
print("Specified -n, will create a new history")
new_history = True
else:
usage()

# state information
var_dir = os.path.join( os.path.expanduser('~'), ".check_galaxy", server )
if not os.access( var_dir, os.F_OK ):
os.makedirs( var_dir, 0700 )
os.makedirs( var_dir, 0o700 )

# default timeout for twill browser is never
socket.setdefaulttimeout(300)
@@ -256,7 +257,7 @@ def wait(self):
def check_state(self):
if self.hda_state != "ok":
self.get("/datasets/%s/stderr" % self.hda_id)
print tc.browser.get_html()
print(tc.browser.get_html())
raise Exception("HDA %s NOT OK: %s" % (self.hda_id, self.hda_state))

def diff(self):
@@ -281,7 +282,7 @@ def delete_datasets(self):
self.get('/datasets/%s/delete' % hda['id'])
hdas = [hda['id'] for hda in self.undeleted_hdas]
if hdas:
print "Remaining datasets ids:", " ".join(hdas)
print("Remaining datasets ids:", " ".join(hdas))
raise Exception("History still contains datasets after attempting to delete them")

def check_if_logged_in(self):
@@ -344,7 +345,7 @@ def handle_data(self, data):

def dprint(str):
if debug:
print str
print(str)

# do stuff here
if __name__ == "__main__":
@@ -360,7 +361,7 @@ def dprint(str):
dprint("not logged in... logging in")
b.login(username, password)

for tool, params in tools.iteritems():
for tool, params in tools.items():

check_file = ""

@@ -388,5 +389,5 @@ def dprint(str):
b.diff()
b.delete_datasets()

print "OK"
print("OK")
sys.exit(0)
@@ -1,5 +1,4 @@
#!/usr/bin/env python

"""
Connects to a UCSC table browser and scrapes chrominfo for every build
specified by an input file (such as one output by parse_builds.py).
@@ -12,18 +11,21 @@
Usage:
python build_chrom_db.py dbpath/ [builds_file]
"""
from __future__ import print_function

import fileinput
import os
import sys
import urllib

from six.moves.urllib.parse import urlencode
from six.moves.urllib.request import urlopen

import parse_builds


def getchrominfo(url, db):
tableURL = "http://genome-test.cse.ucsc.edu/cgi-bin/hgTables?"
URL = tableURL + urllib.urlencode({
URL = tableURL + urlencode({
"clade": "",
"org": "",
"db": db,
@@ -34,7 +36,7 @@ def getchrominfo(url, db):
"hgta_regionType": "",
"position": "",
"hgta_doTopSubmit": "get info"})
page = urllib.urlopen(URL)
page = urlopen(URL)
for line in page:
line = line.rstrip( "\r\n" )
if line.startswith("#"):
@@ -68,12 +70,12 @@ def getchrominfo(url, db):
for build in builds:
if build == "?":
continue # no lengths for unspecified chrom
print "Retrieving " + build
print("Retrieving " + build)
outfile_name = dbpath + build + ".len"
try:
with open(outfile_name, "w") as outfile:
for chrominfo in getchrominfo("http://genome-test.cse.ucsc.edu/cgi-bin/hgTables?", build):
print >> outfile, "\t".join(chrominfo)
print("\t".join(chrominfo), file=outfile)
except Exception as e:
print "Failed to retrieve %s: %s" % (build, e)
print("Failed to retrieve %s: %s" % (build, e))
os.remove(outfile_name)
@@ -1,34 +1,35 @@
#!/usr/bin/env python

"""
Connects to the URL specified and outputs builds available at that
DSN in tabular format. UCSC Main gateway is used as default.
build description
"""
from __future__ import print_function

import sys
import urllib
import xml.etree.ElementTree as ElementTree

from six.moves.urllib.request import urlopen


def getbuilds(url):
try:
page = urllib.urlopen(url)
page = urlopen(url)
except:
print "#Unable to open " + url
print "?\tunspecified (?)"
print("#Unable to open " + url)
print("?\tunspecified (?)")
sys.exit(1)

text = page.read()
try:
tree = ElementTree.fromstring(text)
except:
print "#Invalid xml passed back from " + url
print "?\tunspecified (?)"
print("#Invalid xml passed back from " + url)
print("?\tunspecified (?)")
sys.exit(1)

print "#Harvested from " + url
print "?\tunspecified (?)"
print("#Harvested from " + url)
print("?\tunspecified (?)")
for dsn in tree:
build = dsn.find("SOURCE").attrib['id']
description = dsn.find("DESCRIPTION").text.replace(" - Genome at UCSC", "").replace(" Genome at UCSC", "")
@@ -49,4 +50,4 @@ def getbuilds(url):
else:
URL = "http://genome.cse.ucsc.edu/cgi-bin/das/dsn"
for build in getbuilds(URL):
print build[0] + "\t" + build[1] + " (" + build[0] + ")"
print(build[0] + "\t" + build[1] + " (" + build[0] + ")")
@@ -2,10 +2,12 @@
"""
Connects to sites and determines which builds are available at each.
"""
from __future__ import print_function

import urllib
import xml.etree.ElementTree as ElementTree

from six.moves.urllib.request import urlopen

sites = ['http://genome.ucsc.edu/cgi-bin/',
'http://archaea.ucsc.edu/cgi-bin/',
'http://genome-test.cse.ucsc.edu/cgi-bin/']
@@ -18,27 +20,27 @@ def main():
trackurl = sites[i] + "hgTracks?"
builds = []
try:
page = urllib.urlopen(site)
page = urlopen(site)
except:
print "#Unable to connect to " + site
print("#Unable to connect to " + site)
continue
text = page.read()
try:
tree = ElementTree.fromstring(text)
except:
print "#Invalid xml passed back from " + site
print("#Invalid xml passed back from " + site)
continue
print "#Harvested from", site
print("#Harvested from", site)

for dsn in tree:
build = dsn.find("SOURCE").attrib['id']
builds.append(build)
build_dict = {}
for build in builds:
build_dict[build] = 0
builds = build_dict.keys()
builds = list(build_dict.keys())
yield [names[i], trackurl, builds]

if __name__ == "__main__":
for site in main():
print site[0] + "\t" + site[1] + "\t" + ",".join(site[2])
print(site[0] + "\t" + site[1] + "\t" + ",".join(site[2]))

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