Merge remote-tracking branch 'origin/release_16.07' into release_16.10

lib/galaxy/datatypes/dataproviders/external.py

@@ -8,8 +8,9 @@ import gzip
 import line
 import subprocess
 import tempfile
-import urllib
-import urllib2
+
+from six.moves.urllib.parse import urlencode, urlparse
+from six.moves.urllib.request import urlopen
 
 _TODO = """
 YAGNI: ftp, image, cryptos, sockets
@@ -105,13 +106,16 @@ class URLDataProvider( base.DataProvider ):
         self.method = method
 
         self.data = data or {}
-        encoded_data = urllib.urlencode( self.data )
+        encoded_data = urlencode( self.data )
+
+        scheme = urlparse(url).scheme
+        assert scheme in ('http', 'https', 'ftp'), 'Invalid URL scheme: %s' % scheme
 
         if method == 'GET':
             self.url += '?%s' % ( encoded_data )
-            opened = urllib2.urlopen( url )
+            opened = urlopen( url )
         elif method == 'POST':
-            opened = urllib2.urlopen( url, encoded_data )
+            opened = urlopen( url, encoded_data )
         else:
             raise ValueError( 'Not a valid method: %s' % ( method ) )
 

lib/galaxy/util/__init__.py

@@ -1459,6 +1459,7 @@ def build_url( base_url, port=80, scheme='http', pathspec=None, params=None, dos
     parsed_url = urlparse.urlparse( base_url )
     if scheme != 'http':
         parsed_url.scheme = scheme
+    assert parsed_url.scheme in ('http', 'https', 'ftp'), 'Invalid URL scheme: %s' % scheme
     if port != 80:
         url = '%s://%s:%d/%s' % ( parsed_url.scheme, parsed_url.netloc.rstrip( '/' ), int( port ), parsed_url.path )
     else:

lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py

@@ -6,7 +6,7 @@ import json
 import logging
 import os
 
-from six.moves.urllib.parse import urlencode
+from six.moves.urllib.parse import urlencode, urlparse
 from six.moves.urllib.request import Request, urlopen
 
 from galaxy.util import asbool, build_url, url_get
@@ -380,9 +380,8 @@ class RepositoryDependencyInstallManager( object ):
                     pathspec = [ 'repository', 'get_required_repo_info_dict' ]
                     url = build_url( tool_shed_url, pathspec=pathspec )
                     # Fix for handling 307 redirect not being handled nicely by urlopen() when the Request() has data provided
-                    url = urlopen( Request( url ) ).geturl()
-                    request = Request( url, data=urlencode( dict( encoded_str=encoded_required_repository_str ) ) )
-                    response = urlopen( request ).read()
+                    url = _urlopen(url).geturl()
+                    response = _urlopen(url, urlencode(dict(encoded_str=encoded_required_repository_str))).read()
                     if response:
                         try:
                             required_repo_info_dict = json.loads( response )
@@ -469,3 +468,9 @@ class RepositoryDependencyInstallManager( object ):
         repository.error_message = None
         self.app.install_model.context.add( repository )
         self.app.install_model.context.flush()
+
+
+def _urlopen(url, data=None):
+    scheme = urlparse(url).scheme
+    assert scheme in ('http', 'https', 'ftp'), 'Invalid URL scheme: %s' % scheme
+    return urlopen(Request(url, data))