Make some files compatible with Python3

Also enlarge the set of files tested with flake8 under Python3

.ci/py3_sources.txt

@@ -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 +24,38 @@ 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/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/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/

contrib/galaxy_config_merger.py

@@ -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))

contrib/nagios/check_galaxy.py

@@ -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)

cron/build_chrom_db.py

@@ -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)

cron/parse_builds.py

@@ -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] + ")")

cron/parse_builds_3_sites.py

@@ -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]))