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Fix all E201 and E202 style errors

Browse Source 
using the following command:
```
autopep8 -i -r --exclude $(sed -e 's|^|./|' -e 's|/$||' .ci/flake8_blacklist.txt | paste -sd,) --select E201,E202 .
```
This commit is contained in:
Nicola Soranzo
2017-08-17 11:35:39 +01:00
committed by Nicola Soranzo
parent 008a1d849c
commit 21b44bf348
1062 changed files with 69958 additions and 69959 deletions
Download Patch File Download Diff File Expand all files Collapse all files
scripts/check_galaxy.py
+22 -22
View File
@@ -23,8 +23,8 @@ if "DEBUG" in os.environ:
debug = os.environ["DEBUG"]
else:
debug = False
scripts_dir = os.path.abspath( os.path.dirname( sys.argv[0] ) )
test_data_dir = os.path.join( scripts_dir, os.pardir, "test-data" )
scripts_dir = os.path.abspath(os.path.dirname(sys.argv[0]))
test_data_dir = os.path.join(scripts_dir, os.pardir, "test-data")
# what tools to run - not so pretty
tools = {
"gops_intersect_1":
@@ -32,11 +32,11 @@ tools = {
{
"inputs":
(
os.path.join( test_data_dir, "1.bed" ),
os.path.join( test_data_dir, "2.bed" )
os.path.join(test_data_dir, "1.bed"),
os.path.join(test_data_dir, "2.bed")
)
},
{ "check_file": os.path.join( test_data_dir, "gops_intersect_out.bed" ) },
{"check_file": os.path.join(test_data_dir, "gops_intersect_out.bed")},
{
"tool_run_options":
{
@@ -56,11 +56,11 @@ def usage():
try:
opts, args = getopt.getopt( sys.argv[1:], 'n' )
opts, args = getopt.getopt(sys.argv[1:], 'n')
except getopt.GetoptError as e:
print(str(e))
usage()
if len( args ) < 1:
if len(args) < 1:
usage()
server = args[0]
if server.endswith(".g2.bx.psu.edu"):
@@ -79,14 +79,14 @@ for o, a in opts:
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, 0o700 )
var_dir = os.path.join(os.path.expanduser('~'), ".check_galaxy", server)
if not os.access(var_dir, os.F_OK):
os.makedirs(var_dir, 0o700)
# get user/pass
login_file = os.path.join( var_dir, "login" )
login_file = os.path.join(var_dir, "login")
try:
f = open( login_file, 'r' )
f = open(login_file, 'r')
except:
message = """Please create the file:
%s
@@ -97,7 +97,7 @@ check_galaxy@example.com password
If the user does not exist, check_galaxy will create it for you.""" % login_file
sys.exit(message)
( username, password ) = f.readline().split()
(username, password) = f.readline().split()
# default timeout for twill browser is never
socket.setdefaulttimeout(300)
@@ -118,7 +118,7 @@ class Browser:
self.status = None
self.check_file = None
self.hid = None
self.cookie_jar = os.path.join( var_dir, "cookie_jar" )
self.cookie_jar = os.path.join(var_dir, "cookie_jar")
dprint("cookie jar path: %s" % self.cookie_jar)
if not os.access(self.cookie_jar, os.R_OK):
dprint("no cookie jar at above path, creating")
@@ -140,7 +140,7 @@ class Browser:
p = didParser()
p.feed(tc.browser.get_html())
if len(p.dids) > 0:
print("Remaining datasets ids:", " ".join( p.dids ))
print("Remaining datasets ids:", " ".join(p.dids))
raise Exception("History still contains datasets after attempting to delete them")
if new_history:
self.get("/history/delete_current")
@@ -152,16 +152,16 @@ class Browser:
tc.go(url)
tc.code(302)
tc.get_browser()._browser.set_handle_redirect(True)
dprint( "%s is returning redirect (302)" % url )
dprint("%s is returning redirect (302)" % url)
return(True)
except twill.errors.TwillAssertionError as e:
tc.get_browser()._browser.set_handle_redirect(True)
dprint( "%s is not returning redirect (302): %s" % (url, e) )
dprint("%s is not returning redirect (302): %s" % (url, e))
code = tc.browser.get_code()
if code == 502:
is_maint = self.check_maint()
if is_maint:
dprint( "Galaxy is down, but a maint file was found, so not sending alert" )
dprint("Galaxy is down, but a maint file was found, so not sending alert")
sys.exit(0)
else:
sys.exit("Galaxy is down (code 502)")
@@ -232,8 +232,8 @@ class Browser:
count += 1
self.get("/root/history")
page = tc.browser.get_html()
if page.find( '<!-- running: do not change this comment, used by TwillTestCase.wait -->' ) > -1:
time.sleep( sleep_amount )
if page.find('<!-- running: do not change this comment, used by TwillTestCase.wait -->') > -1:
time.sleep(sleep_amount)
sleep_amount += 1
else:
break
@@ -340,7 +340,7 @@ class didParser(htmllib.HTMLParser):
def start_div(self, attrs):
for i in attrs:
if i[0] == "id" and i[1].startswith("historyItemContainer-"):
self.dids.append( i[1].rsplit("historyItemContainer-", 1)[1] )
self.dids.append(i[1].rsplit("historyItemContainer-", 1)[1])
dprint("got a dataset id: %s" % self.dids[-1])
@@ -360,7 +360,7 @@ class loggedinParser(htmllib.HTMLParser):
if self.in_p:
if data == "You are currently not logged in.":
self.logged_in = False
elif data.startswith( "You are currently logged in as " ):
elif data.startswith("You are currently logged in as "):
self.logged_in = True