diff --git a/lib/galaxy/util/__init__.py b/lib/galaxy/util/__init__.py
index be904c17afc..3478801d726 100644
--- a/lib/galaxy/util/__init__.py
+++ b/lib/galaxy/util/__init__.py
@@ -30,6 +30,7 @@ from xml.etree import ElementInclude, ElementTree
 from six import binary_type, iteritems, PY3, string_types, text_type
 from six.moves import email_mime_text, xrange, zip
 from six.moves.urllib import parse as urlparse
+from six.moves.urllib import request as urlrequest
 
 try:
     import docutils.core as docutils_core
@@ -1342,6 +1343,46 @@ def parse_int(value, min_val=None, max_val=None, default=None, allow_none=False)
             raise
 
 
+def build_url( base_url, port=80, scheme='http', pathspec=None, params=None, doseq=False ):
+    if params is None:
+        params = dict()
+    if pathspec is None:
+        pathspec = []
+    parsed_url = urlparse.urlparse( base_url )
+    if scheme != 'http':
+        parsed_url.scheme = scheme
+    if port != 80:
+        url = '%s://%s:%d/%s' % ( parsed_url.scheme, parsed_url.netloc.rstrip( '/' ), int( port ), parsed_url.path )
+    else:
+        url = '%s://%s/%s' % ( parsed_url.scheme, parsed_url.netloc.rstrip( '/' ), parsed_url.path.lstrip( '/' ) )
+    if len( pathspec ) > 0:
+        url = '%s/%s' % ( url.rstrip( '/' ), '/'.join( pathspec ) )
+    if parsed_url.query:
+        for query_parameter in parsed_url.query.split( '&' ):
+            key, value = query_parameter.split( '=' )
+            params[ key ] = value
+    if params:
+        url += '?%s' % urlparse.urlencode( params, doseq=doseq )
+    return url
+
+
+def url_get( base_url, password_mgr=None, pathspec=None, params=None ):
+    """Make contact with the uri provided and return any contents."""
+    # Uses system proxy settings if they exist.
+    proxy = urlrequest.ProxyHandler()
+    if password_mgr is not None:
+        auth = urlrequest.HTTPDigestAuthHandler( password_mgr )
+        urlopener = urlrequest.build_opener( proxy, auth )
+    else:
+        urlopener = urlrequest.build_opener( proxy )
+    urlrequest.install_opener( urlopener )
+    full_url = build_url( base_url, pathspec=pathspec, params=params )
+    response = urlopener.open( full_url )
+    content = response.read()
+    response.close()
+    return content
+
+
 def safe_relpath(path):
     """
     Given what we expect to be a relative path, determine whether the path
diff --git a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
index 215cd0b7b3c..d771b998f58 100644
--- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
+++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
@@ -13,7 +13,6 @@ from galaxy.web.base.controller import BaseAPIController
 from tool_shed.galaxy_install.install_manager import InstallRepositoryManager
 from tool_shed.galaxy_install.metadata.installed_repository_metadata_manager import InstalledRepositoryMetadataManager
 from tool_shed.galaxy_install.repair_repository_manager import RepairRepositoryManager
-from tool_shed.util import common_util
 from tool_shed.util import encoding_util
 from tool_shed.util import hg_util
 from tool_shed.util import workflow_util
@@ -100,7 +99,7 @@ class ToolShedRepositoriesController( BaseAPIController ):
         params = dict(name=name, owner=owner)
         pathspec = ['api', 'repositories', 'get_ordered_installable_revisions']
         try:
-            raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, pathspec, params )
+            raw_text = util.url_get( tool_shed_url, password_mgr=self.app.tool_shed_registry.url_auth( tool_shed_url ), pathspec=pathspec, params=params )
         except Exception, e:
             message = "Error attempting to retrieve the latest installable revision from tool shed %s for repository %s owned by %s: %s" % \
                 ( str( tool_shed_url ), str( name ), str( owner ), str( e ) )
diff --git a/lib/galaxy/webapps/galaxy/controllers/admin.py b/lib/galaxy/webapps/galaxy/controllers/admin.py
index 1f6109fb759..d3c1414c549 100644
--- a/lib/galaxy/webapps/galaxy/controllers/admin.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin.py
@@ -11,7 +11,7 @@ from galaxy.actions.admin import AdminActions
 from galaxy.exceptions import MessageException
 from galaxy.model import tool_shed_install as install_model
 from galaxy.model.util import pgcalc
-from galaxy.util import nice_size, sanitize_text
+from galaxy.util import nice_size, sanitize_text, url_get
 from galaxy.util.odict import odict
 from galaxy.web import url_for
 from galaxy.web.base.controller import BaseUIController, UsesQuotaMixin
@@ -770,9 +770,9 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuotaMixin, QuotaP
         tree = galaxy.util.parse_xml( tools_xml_file_path )
         root = tree.getroot()
         tool_shed = root.get( 'name' )
-        tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, tool_shed )
+        shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, tool_shed )
         repo_name_dependency_tups = []
-        if tool_shed_url:
+        if shed_url:
             for elem in root:
                 if elem.tag == 'repository':
                     tool_dependencies = []
@@ -781,7 +781,7 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuotaMixin, QuotaP
                     changeset_revision = elem.get( 'changeset_revision' )
                     params = dict( name=repository_name, owner='devteam', changeset_revision=changeset_revision )
                     pathspec = [ 'repository', 'get_tool_dependencies' ]
-                    text = common_util.tool_shed_get( trans.app, tool_shed_url, pathspec=pathspec, params=params )
+                    text = url_get( shed_url, password_mgr=self.app.tool_shed_registry.url_auth( shed_url ), pathspec=pathspec, params=params )
                     if text:
                         tool_dependencies_dict = encoding_util.tool_shed_decode( text )
                         for dependency_key, requirements_dict in tool_dependencies_dict.items():
diff --git a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
index 4ca6110d570..624a26069df 100644
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -189,7 +189,7 @@ class AdminToolshed( AdminGalaxy ):
         tool_shed_url = kwd.get( 'tool_shed_url', '' )
         tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, tool_shed_url )
         params = dict( galaxy_url=web.url_for( '/', qualified=True ) )
-        url = common_util.url_join( tool_shed_url, pathspec=[ 'repository', 'browse_valid_categories' ], params=params )
+        url = util.build_url( tool_shed_url, pathspec=[ 'repository', 'browse_valid_categories' ], params=params )
         return trans.response.send_redirect( url )
 
     @web.expose
@@ -212,7 +212,7 @@ class AdminToolshed( AdminGalaxy ):
                        owner=str( repository.owner ),
                        changeset_revision=str( repository.changeset_revision ) )
         pathspec = [ 'repository', 'check_for_updates' ]
-        url = common_util.url_join( tool_shed_url, pathspec=pathspec, params=params )
+        url = util.build_url( tool_shed_url, pathspec=pathspec, params=params )
         return trans.response.send_redirect( url )
 
     @web.expose
@@ -369,7 +369,7 @@ class AdminToolshed( AdminGalaxy ):
         tool_shed_url = kwd.get( 'tool_shed_url', '' )
         tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, tool_shed_url )
         params = dict( galaxy_url=web.url_for( '/', qualified=True ) )
-        url = common_util.url_join( tool_shed_url, pathspec=[ 'repository', 'find_tools' ], params=params )
+        url = util.build_url( tool_shed_url, pathspec=[ 'repository', 'find_tools' ], params=params )
         return trans.response.send_redirect( url )
 
     @web.expose
@@ -378,7 +378,7 @@ class AdminToolshed( AdminGalaxy ):
         tool_shed_url = kwd.get( 'tool_shed_url', '' )
         tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, tool_shed_url )
         params = dict( galaxy_url=web.url_for( '/', qualified=True ) )
-        url = common_util.url_join( tool_shed_url, pathspec=[ 'repository', 'find_workflows' ], params=params )
+        url = util.build_url( tool_shed_url, pathspec=[ 'repository', 'find_workflows' ], params=params )
         return trans.response.send_redirect( url )
 
     @web.expose
@@ -413,7 +413,7 @@ class AdminToolshed( AdminGalaxy ):
             raise Exception( message )
         params = dict( name=repository_name, owner=repository_owner, changeset_revision=changeset_revision )
         pathspec = [ 'repository', 'get_tool_dependencies' ]
-        raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, pathspec=pathspec, params=params )
+        raw_text = util.url_get( tool_shed_url, password_mgr=self.app.tool_shed_registry.url_auth( tool_shed_url ), pathspec=pathspec, params=params )
         if len( raw_text ) > 2:
             encoded_text = json.loads( raw_text )
             text = encoding_util.tool_shed_decode( encoded_text )
@@ -439,7 +439,7 @@ class AdminToolshed( AdminGalaxy ):
                        owner=str( repository_owner ),
                        changeset_revision=changeset_revision )
         pathspec = [ 'repository', 'get_updated_repository_information' ]
-        raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, pathspec=pathspec, params=params )
+        raw_text = util.url_get( tool_shed_url, password_mgr=self.app.tool_shed_registry.url_auth( tool_shed_url ), pathspec=pathspec, params=params )
         repo_information_dict = json.loads( raw_text )
         return repo_information_dict
 
@@ -529,8 +529,8 @@ class AdminToolshed( AdminGalaxy ):
                                name=name,
                                owner=owner )
                 pathspec = [ 'repository', 'get_latest_downloadable_changeset_revision' ]
-                raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, pathspec=pathspec, params=params )
-                url = common_util.url_join( tool_shed_url, pathspec=pathspec, params=params )
+                raw_text = util.url_get( tool_shed_url, password_mgr=self.app.tool_shed_registry.url_auth( tool_shed_url ), pathspec=pathspec, params=params )
+                url = util.build_url( tool_shed_url, pathspec=pathspec, params=params )
                 latest_downloadable_revision = json.loads( raw_text )
                 if latest_downloadable_revision == hg_util.INITIAL_CHANGELOG_HASH:
                     message = 'Error retrieving the latest downloadable revision for this repository via the url <b>%s</b>.' % url
@@ -541,7 +541,7 @@ class AdminToolshed( AdminGalaxy ):
                     # appropriate repository revision if one exists.  We need to create a temporary repo_info_tuple
                     # with the following entries to handle this.
                     # ( description, clone_url, changeset_revision, ctx_rev, owner, repository_dependencies, tool_dependencies )
-                    tmp_clone_url = common_util.url_join( tool_shed_url, pathspec=[ 'repos', owner, name ] )
+                    tmp_clone_url = util.build_url( tool_shed_url, pathspec=[ 'repos', owner, name ] )
                     tmp_repo_info_tuple = ( None, tmp_clone_url, latest_downloadable_revision, None, owner, None, None )
                     installed_repository, installed_changeset_revision = \
                         suc.repository_was_previously_installed( trans.app, tool_shed_url, name, tmp_repo_info_tuple, from_tip=False )
@@ -559,7 +559,7 @@ class AdminToolshed( AdminGalaxy ):
                                        changeset_revisions=str( latest_downloadable_revision ),
                                        galaxy_url=web.url_for( '/', qualified=True ) )
                         pathspec = [ 'repository', 'install_repositories_by_revision' ]
-                        url = common_util.url_join( tool_shed_url, pathspec=pathspec, params=params )
+                        url = util.build_url( tool_shed_url, pathspec=pathspec, params=params )
                         return trans.response.send_redirect( url )
             else:
                 message = 'Cannot locate installed tool shed repository with encoded id <b>%s</b>.' % str( repository_id )
@@ -727,7 +727,7 @@ class AdminToolshed( AdminGalaxy ):
                            changeset_revisions=installed_changeset_revision,
                            galaxy_url=web.url_for( '/', qualified=True ) )
             pathspec = [ 'repository', 'install_repositories_by_revision' ]
-            url = common_util.url_join( tool_shed_url, pathspec=pathspec, params=params )
+            url = util.build_url( tool_shed_url, pathspec=pathspec, params=params )
             return trans.response.send_redirect( url )
         description = kwd.get( 'description', repository.description )
         shed_tool_conf, tool_path, relative_install_dir = suc.get_tool_panel_config_tool_path_install_dir( trans.app, repository )
@@ -985,7 +985,7 @@ class AdminToolshed( AdminGalaxy ):
                 try:
                     params = dict( name=str( repository.name ), owner=str( repository.owner ) )
                     pathspec = [ 'repository', 'get_repository_id' ]
-                    repository_ids = common_util.tool_shed_get( trans.app, tool_shed_url, pathspec=pathspec, params=params )
+                    repository_ids = util.url_get( tool_shed_url, password_mgr=self.app.tool_shed_registry.url_auth( tool_shed_url ), pathspec=pathspec, params=params )
                 except Exception, e:
                     # The Tool Shed cannot handle the get_repository_id request, so the code must be older than the
                     # 04/2014 Galaxy release when it was introduced.  It will be safest to error out and let the
@@ -1005,7 +1005,7 @@ class AdminToolshed( AdminGalaxy ):
             # Get the information necessary to install each repository.
             params = dict( repository_ids=str( repository_ids ), changeset_revisions=str( changeset_revisions ) )
             pathspec = [ 'repository', 'get_repository_information' ]
-            raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, pathspec=pathspec, params=params )
+            raw_text = util.url_get( tool_shed_url, password_mgr=self.app.tool_shed_registry.url_auth( tool_shed_url ), pathspec=pathspec, params=params )
             repo_information_dict = json.loads( raw_text )
             for encoded_repo_info_dict in repo_information_dict.get( 'repo_info_dicts', [] ):
                 decoded_repo_info_dict = encoding_util.tool_shed_decode( encoded_repo_info_dict )
@@ -1539,7 +1539,7 @@ class AdminToolshed( AdminGalaxy ):
                                owner=tool_shed_repository.owner,
                                changeset_revision=tool_shed_repository.installed_changeset_revision )
                 pathspec = [ 'repository', 'get_readme_files' ]
-                raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, pathspec=pathspec, params=params )
+                raw_text = util.url_get( tool_shed_url, password_mgr=self.app.tool_shed_registry.url_auth( tool_shed_url ), pathspec=pathspec, params=params )
                 readme_files_dict = json.loads( raw_text )
                 tool_dependencies = metadata.get( 'tool_dependencies', None )
             rdim = repository_dependency_manager.RepositoryDependencyInstallManager( trans.app )
@@ -1739,7 +1739,7 @@ class AdminToolshed( AdminGalaxy ):
         tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, str( repository.tool_shed ) )
         params = dict( name=repository.name, owner=repository.owner, changeset_revision=repository.changeset_revision )
         pathspec = [ 'repository', 'get_tool_versions' ]
-        text = common_util.tool_shed_get( trans.app, tool_shed_url, pathspec=pathspec, params=params )
+        text = util.url_get( tool_shed_url, password_mgr=self.app.tool_shed_registry.url_auth( tool_shed_url ), pathspec=pathspec, params=params )
         if text:
             tool_version_dicts = json.loads( text )
             tvm = tool_version_manager.ToolVersionManager( trans.app )
diff --git a/lib/galaxy/webapps/galaxy/controllers/workflow.py b/lib/galaxy/webapps/galaxy/controllers/workflow.py
index c92a5fbf878..7fcfa825131 100644
--- a/lib/galaxy/webapps/galaxy/controllers/workflow.py
+++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py
@@ -10,7 +10,6 @@ from sqlalchemy import and_
 from sqlalchemy.sql import expression
 from markupsafe import escape
 
-from tool_shed.util import common_util
 from tool_shed.util import encoding_util
 
 from galaxy import model
@@ -862,7 +861,7 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
                            workflow_name=encoding_util.tool_shed_encode( workflow_name ),
                            open_for_url=True )
             pathspec = [ 'workflow', 'import_workflow' ]
-            workflow_text = common_util.tool_shed_get( trans.app, tool_shed_url, pathspec=pathspec, params=params )
+            workflow_text = util.url_get( tool_shed_url, password_mgr=self.app.tool_shed_registry.url_auth( tool_shed_url ), pathspec=pathspec, params=params )
             import_button = True
         if import_button:
             workflow_data = None
diff --git a/lib/galaxy/webapps/tool_shed/controllers/repository.py b/lib/galaxy/webapps/tool_shed/controllers/repository.py
index df8530c33f0..646d470f823 100644
--- a/lib/galaxy/webapps/tool_shed/controllers/repository.py
+++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py
@@ -809,7 +809,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
                     return update
         params['latest_changeset_revision'] = str( latest_changeset_revision )
         params['latest_ctx_rev'] = str( update_to_ctx.rev() )
-        url = common_util.url_join( galaxy_url, pathspec=pathspec, params=params )
+        url = util.build_url( galaxy_url, pathspec=pathspec, params=params )
         return trans.response.send_redirect( url )
 
     @web.expose
@@ -1065,7 +1065,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
         trans.sa_session.flush()
         tool_shed_url = web.url_for( '/', qualified=True )
         pathspec = [ 'repos', str( repository.user.username ), str( repository.name ), 'archive', file_type_str ]
-        download_url = common_util.url_join( tool_shed_url, pathspec=pathspec )
+        download_url = util.build_url( tool_shed_url, pathspec=pathspec )
         return trans.response.send_redirect( download_url )
 
     @web.expose
@@ -1534,7 +1534,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
                         time_tested = repository_metadata.time_last_tested.strftime( '%a, %d %b %Y %H:%M:%S UT' )
                     # Generate a citable URL for this repository with owner and changeset revision.
                     pathspec = [ 'view', str( user.username ), str( repository.name ), str( repository_metadata.changeset_revision ) ]
-                    repository_citable_url = common_util.url_join( tool_shed_url, pathspec=pathspec )
+                    repository_citable_url = util.build_url( tool_shed_url, pathspec=pathspec )
                     passed_tests = len( tool_test_results.get( 'passed_tests', [] ) )
                     failed_tests = len( tool_test_results.get( 'failed_tests', [] ) )
                     missing_test_components = len( tool_test_results.get( 'missing_test_components', [] ) )
@@ -1982,7 +1982,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
                            repository_ids=','.join( util.listify( repository_ids ) ),
                            changeset_revisions=','.join( util.listify( changeset_revisions ) ) )
             pathspec = [ 'admin_toolshed', 'prepare_for_install' ]
-            url = common_util.url_join( galaxy_url, pathspec=pathspec, params=params )
+            url = util.build_url( galaxy_url, pathspec=pathspec, params=params )
             return trans.response.send_redirect( url )
         else:
             message = 'Repository installation is not possible due to an invalid Galaxy URL: <b>%s</b>.  ' % galaxy_url
diff --git a/lib/tool_shed/capsule/capsule_manager.py b/lib/tool_shed/capsule/capsule_manager.py
index 7dd879bf6eb..5fcd84c5b18 100644
--- a/lib/tool_shed/capsule/capsule_manager.py
+++ b/lib/tool_shed/capsule/capsule_manager.py
@@ -15,6 +15,7 @@ from galaxy import web
 from galaxy.util import asbool
 from galaxy.util import CHUNK_SIZE
 from galaxy.util import safe_relpath
+from galaxy.util import build_url
 from galaxy.util.odict import odict
 from tool_shed.dependencies.repository.relation_builder import RelationBuilder
 from tool_shed.dependencies import attribute_handlers
@@ -123,7 +124,7 @@ class ExportRepositoryManager( object ):
             params = dict( encoded_repositories_archive_name=encoded_repositories_archive_name )
             pathspec = [ 'repository', 'export_via_api' ]
             tool_shed_url = web.url_for( '/', qualified=True )
-            download_url = common_util.url_join( tool_shed_url, pathspec=pathspec, params=params )
+            download_url = build_url( tool_shed_url, pathspec=pathspec, params=params )
             return dict( download_url=download_url, error_messages=error_messages )
         return repositories_archive, error_messages
 
diff --git a/lib/tool_shed/galaxy_install/dependency_display.py b/lib/tool_shed/galaxy_install/dependency_display.py
index 3b92497f521..b5600bf3c66 100644
--- a/lib/tool_shed/galaxy_install/dependency_display.py
+++ b/lib/tool_shed/galaxy_install/dependency_display.py
@@ -455,7 +455,7 @@ class DependencyDisplayer( object ):
                                    owner=str( repository.owner ),
                                    changeset_revision=str( repository.installed_changeset_revision ) )
                     pathspec = [ 'repository', 'get_readme_files' ]
-                    raw_text = common_util.tool_shed_get( self.app, tool_shed_url, pathspec=pathspec, params=params )
+                    raw_text = util.url_get( tool_shed_url, password_mgr=self.app.tool_shed_registry.url_auth( tool_shed_url ), pathspec=pathspec, params=params )
                     readme_files_dict = json.loads( raw_text )
                 else:
                     readme_files_dict = readme_util.build_readme_files_dict( self.app,
diff --git a/lib/tool_shed/galaxy_install/install_manager.py b/lib/tool_shed/galaxy_install/install_manager.py
index 8351a935777..a03d8e72979 100644
--- a/lib/tool_shed/galaxy_install/install_manager.py
+++ b/lib/tool_shed/galaxy_install/install_manager.py
@@ -460,7 +460,7 @@ class InstallRepositoryManager( object ):
                        changeset_revision=str( changeset_revision ) )
         pathspec = [ 'api', 'repositories', 'get_repository_revision_install_info' ]
         try:
-            raw_text = common_util.tool_shed_get( self.app, tool_shed_url, pathspec=pathspec, params=params )
+            raw_text = util.url_get( tool_shed_url, password_mgr=self.app.tool_shed_registry.url_auth( tool_shed_url ), pathspec=pathspec, params=params )
         except Exception, e:
             message = "Error attempting to retrieve installation information from tool shed "
             message += "%s for revision %s of repository %s owned by %s: %s" % \
@@ -1005,8 +1005,8 @@ def fetch_tool_versions( app, tool_shed_repository ):
                        owner=str( tool_shed_repository.owner ),
                        changeset_revision=str( tool_shed_repository.changeset_revision ) )
         pathspec = [ 'repository', 'get_tool_versions' ]
-        url = common_util.url_join( tool_shed_url, pathspec=pathspec, params=params )
-        text = common_util.tool_shed_get( app, tool_shed_url, pathspec=pathspec, params=params )
+        url = util.build_url( tool_shed_url, pathspec=pathspec, params=params )
+        text = util.url_get( tool_shed_url, password_mgr=app.tool_shed_registry.url_auth( tool_shed_url ), pathspec=pathspec, params=params )
         if text:
             return json.loads( text )
         else:
diff --git a/lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py b/lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
index b03417da16f..a69c0357aec 100644
--- a/lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
+++ b/lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
@@ -8,7 +8,7 @@ import os
 import urllib
 import urllib2
 
-from galaxy.util import asbool
+from galaxy.util import asbool, url_get, build_url
 
 from tool_shed.galaxy_install.tools import tool_panel_manager
 
@@ -291,9 +291,9 @@ class RepositoryDependencyInstallManager( object ):
                        changeset_revision=str( repository.changeset_revision ) )
         pathspec = [ 'repository', 'get_repository_dependencies' ]
         try:
-            raw_text = common_util.tool_shed_get( app, tool_shed_url, pathspec=pathspec, params=params )
+            raw_text = url_get( tool_shed_url, password_mgr=app.tool_shed_registry.url_auth( tool_shed_url ), pathspec=pathspec, params=params )
         except Exception, e:
-            log.error("The URL\n%s\nraised the exception:\n%s\n", common_util.url_join( tool_shed_url, pathspec=pathspec, params=params ), str( e ) )
+            log.error("The URL\n%s\nraised the exception:\n%s\n", build_url( tool_shed_url, pathspec=pathspec, params=params ), str( e ) )
             return ''
         if len( raw_text ) > 2:
             encoded_text = json.loads( raw_text )
@@ -378,7 +378,7 @@ class RepositoryDependencyInstallManager( object ):
                         # Handle secure / insecure Tool Shed URL protocol changes and port changes.
                         tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( self.app, tool_shed_url )
                     pathspec = [ 'repository', 'get_required_repo_info_dict' ]
-                    url = common_util.url_join( tool_shed_url, pathspec=pathspec )
+                    url = build_url( tool_shed_url, pathspec=pathspec )
                     # Fix for handling 307 redirect not being handled nicely by urllib2.urlopen when the urllib2.Request has data provided
                     url = urllib2.urlopen( urllib2.Request( url ) ).geturl()
                     request = urllib2.Request( url, data=urllib.urlencode( dict( encoded_str=encoded_required_repository_str ) ) )
diff --git a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
index 2198ceb8512..d505325a8be 100644
--- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
+++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
@@ -3,7 +3,7 @@ import os
 import tempfile
 
 from galaxy.tools.deps.resolvers import INDETERMINATE_DEPENDENCY
-from galaxy.util import listify
+from galaxy.util import listify, url_get
 from tool_shed.util import basic_util
 from tool_shed.util import common_util
 from tool_shed.util import shed_util_common as suc
@@ -249,7 +249,7 @@ class Repository( RecipeTag, SyncDatabase ):
                        owner=owner,
                        changeset_revision=changeset_revision )
         pathspec = [ 'repository', 'get_tool_dependencies_config_contents' ]
-        text = common_util.tool_shed_get( self.app, tool_shed_url, pathspec=pathspec, params=params )
+        text = url_get( tool_shed_url, password_mgr=self.app.tool_shed_registry.url_auth( tool_shed_url ), pathspec=pathspec, params=params )
         if text:
             # Write the contents to a temporary file on disk so it can be reloaded and parsed.
             fh = tempfile.NamedTemporaryFile( 'wb', prefix="tmp-toolshed-cttdc"  )
diff --git a/lib/tool_shed/galaxy_install/tool_migration_manager.py b/lib/tool_shed/galaxy_install/tool_migration_manager.py
index 64842c07d1f..104a0d84547 100644
--- a/lib/tool_shed/galaxy_install/tool_migration_manager.py
+++ b/lib/tool_shed/galaxy_install/tool_migration_manager.py
@@ -581,7 +581,7 @@ class ToolMigrationManager( object ):
                                    owner=self.repository_owner,
                                    changeset_revision=tool_shed_repository.installed_changeset_revision )
                     pathspec = [ 'repository', 'get_tool_versions' ]
-                    text = common_util.tool_shed_get( self.app, self.tool_shed_url, pathspec=pathspec, params=params )
+                    text = util.url_get( self.tool_shed_url, password_mgr=self.app.tool_shed_registry.url_auth( self.tool_shed_url ), pathspec=pathspec, params=params )
                     if text:
                         tool_version_dicts = json.loads( text )
                         tvm.handle_tool_versions( tool_version_dicts, tool_shed_repository )
diff --git a/lib/tool_shed/galaxy_install/update_repository_manager.py b/lib/tool_shed/galaxy_install/update_repository_manager.py
index 824f5237e10..aa8e60e9b61 100644
--- a/lib/tool_shed/galaxy_install/update_repository_manager.py
+++ b/lib/tool_shed/galaxy_install/update_repository_manager.py
@@ -9,6 +9,7 @@ from sqlalchemy import false
 import tool_shed.util.shed_util_common as suc
 from tool_shed.util import common_util
 from tool_shed.util import encoding_util
+from galaxy import util
 
 log = logging.getLogger( __name__ )
 
@@ -36,7 +37,7 @@ class UpdateRepositoryManager( object ):
                        changeset_revision=str( repository.installed_changeset_revision ) )
         pathspec = [ 'repository', 'get_changeset_revision_and_ctx_rev' ]
         try:
-            encoded_update_dict = common_util.tool_shed_get( self.app, tool_shed_url, pathspec=pathspec, params=params )
+            encoded_update_dict = util.url_get( tool_shed_url, password_mgr=self.app.tool_shed_registry.url_auth( tool_shed_url ), pathspec=pathspec, params=params )
             if encoded_update_dict:
                 update_dict = encoding_util.tool_shed_decode( encoded_update_dict )
                 includes_data_managers = update_dict.get( 'includes_data_managers', False )
diff --git a/lib/tool_shed/scripts/api/common.py b/lib/tool_shed/scripts/api/common.py
index 02e2b3b1a6a..88f7fcf2e94 100644
--- a/lib/tool_shed/scripts/api/common.py
+++ b/lib/tool_shed/scripts/api/common.py
@@ -6,7 +6,8 @@ import urllib2
 
 sys.path.insert(1, os.path.join( os.path.dirname( __file__ ), os.pardir, os.pardir, os.pardir ) )
 
-from tool_shed.util import common_util, hg_util
+from tool_shed.util import hg_util
+from galaxy import util
 
 
 class HTTPRedirectWithDataHandler( urllib2.HTTPRedirectHandler ):
@@ -131,7 +132,7 @@ def get_api_url( base, parts=[], params=None ):
         parts.insert( 0, 'api' )
     elif 'api' not in parts:
         parts.insert( 0, 'api' )
-    url = common_util.url_join( base, pathspec=parts, params=params )
+    url = util.build_url( base, pathspec=parts, params=params )
     return url
 
 
diff --git a/lib/tool_shed/scripts/deprecate_repositories_without_metadata.py b/lib/tool_shed/scripts/deprecate_repositories_without_metadata.py
index ed86ce60be8..3f090f2edba 100644
--- a/lib/tool_shed/scripts/deprecate_repositories_without_metadata.py
+++ b/lib/tool_shed/scripts/deprecate_repositories_without_metadata.py
@@ -19,7 +19,7 @@ from sqlalchemy import and_, distinct, false, not_
 import galaxy.webapps.tool_shed.config as tool_shed_config
 import galaxy.webapps.tool_shed.model.mapping
 from galaxy.util import send_mail as galaxy_send_mail
-from tool_shed.util.common_util import url_join
+from galaxy.util import build_url
 
 log = logging.getLogger()
 log.setLevel( 10 )
@@ -28,7 +28,7 @@ assert sys.version_info[:2] >= ( 2, 4 )
 
 
 def build_citable_url( host, repository ):
-    return url_join( host, pathspec=[ 'view', repository.user.username, repository.name ] )
+    return build_url( host, pathspec=[ 'view', repository.user.username, repository.name ] )
 
 
 def main():
diff --git a/lib/tool_shed/tool_shed_registry.py b/lib/tool_shed/tool_shed_registry.py
index 5b26bf62395..6014ee5b414 100644
--- a/lib/tool_shed/tool_shed_registry.py
+++ b/lib/tool_shed/tool_shed_registry.py
@@ -1,8 +1,8 @@
 import logging
-import urllib2
 
 from galaxy.util.odict import odict
 from tool_shed.util import common_util, xml_util
+from six.moves.urllib import request as urlrequest
 
 log = logging.getLogger( __name__ )
 
@@ -31,7 +31,7 @@ class Registry( object ):
                             self.tool_sheds_auth[ name ] = None
                             log.debug( 'Loaded reference to tool shed: %s' % name )
                         if name and url and username and password:
-                            pass_mgr = urllib2.HTTPPasswordMgrWithDefaultRealm()
+                            pass_mgr = urlrequest.HTTPPasswordMgrWithDefaultRealm()
                             pass_mgr.add_password( None, url, username, password )
                             self.tool_sheds_auth[ name ] = pass_mgr
                     except Exception, e:
@@ -40,7 +40,7 @@ class Registry( object ):
     def password_manager_for_url( self, url ):
         """
         If the tool shed is using external auth, the client to the tool shed must authenticate to that
-        as well.  This provides access to the urllib2.HTTPPasswordMgrWithdefaultRealm() object for the
+        as well.  This provides access to the six.moves.urllib.request.HTTPPasswordMgrWithdefaultRealm() object for the
         url passed in.
 
         Following more what galaxy.demo_sequencer.controllers.common does might be more appropriate at
@@ -53,3 +53,8 @@ class Registry( object ):
                 return self.tool_sheds_auth[ shed_name ]
         log.debug( "Invalid url '%s' received by tool shed registry's password_manager_for_url method." % str( url ) )
         return None
+
+    def url_auth( self, url ):
+        password_manager = self.password_manager_for_url( url )
+        if password_manager is not None:
+            return urlrequest.HTTPBasicAuthHandler( password_manager )
diff --git a/lib/tool_shed/util/common_util.py b/lib/tool_shed/util/common_util.py
index a3d5f6561ce..2db00a001ea 100644
--- a/lib/tool_shed/util/common_util.py
+++ b/lib/tool_shed/util/common_util.py
@@ -1,9 +1,6 @@
 import json
 import logging
 import os
-import urllib
-import urllib2
-from six import string_types
 
 from galaxy import util
 from galaxy.util.odict import odict
@@ -114,7 +111,7 @@ def check_tool_tag_set( elem, migrated_tool_configs_dict, missing_tool_configs_d
 def generate_clone_url_for_installed_repository( app, repository ):
     """Generate the URL for cloning a repository that has been installed into a Galaxy instance."""
     tool_shed_url = get_tool_shed_url_from_tool_shed_registry( app, str( repository.tool_shed ) )
-    return url_join( tool_shed_url, pathspec=[ 'repos', str( repository.owner ), str( repository.name ) ] )
+    return util.build_url( tool_shed_url, pathspec=[ 'repos', str( repository.owner ), str( repository.name ) ] )
 
 
 def generate_clone_url_for_repository_in_tool_shed( user, repository ):
@@ -135,7 +132,7 @@ def generate_clone_url_from_repo_info_tup( app, repo_info_tup ):
         parse_repository_dependency_tuple( repo_info_tup )
     tool_shed_url = get_tool_shed_url_from_tool_shed_registry( app, toolshed )
     # Don't include the changeset_revision in clone urls.
-    return url_join( tool_shed_url, pathspec=[ 'repos', owner, name ] )
+    return util.build_url( tool_shed_url, pathspec=[ 'repos', owner, name ] )
 
 
 def get_non_shed_tool_panel_configs( app ):
@@ -160,11 +157,11 @@ def get_repository_dependencies( app, tool_shed_url, repository_name, repository
     params = dict( name=repository_name, owner=repository_owner, changeset_revision=changeset_revision )
     pathspec = [ 'repository', 'get_repository_dependencies' ]
     try:
-        raw_text = tool_shed_get( app, tool_shed_url, pathspec=pathspec, params=params )
+        raw_text = util.url_get( tool_shed_url, password_mgr=app.tool_shed_registry.url_auth( tool_shed_url ), pathspec=pathspec, params=params )
         tool_shed_accessible = True
     except Exception, e:
         tool_shed_accessible = False
-        log.warn( "The URL\n%s\nraised the exception:\n%s\n", url_join( tool_shed_url, pathspec=pathspec, params=params ), e )
+        log.warn( "The URL\n%s\nraised the exception:\n%s\n", util.build_url( tool_shed_url, pathspec=pathspec, params=params ), e )
     if tool_shed_accessible:
         if len( raw_text ) > 2:
             encoded_text = json.loads( raw_text )
@@ -192,11 +189,11 @@ def get_tool_dependencies( app, tool_shed_url, repository_name, repository_owner
     params = dict( name=repository_name, owner=repository_owner, changeset_revision=changeset_revision )
     pathspec = [ 'repository', 'get_tool_dependencies' ]
     try:
-        text = tool_shed_get( app, tool_shed_url, pathspec=pathspec, params=params )
+        text = util.url_get( tool_shed_url, password_mgr=app.tool_shed_registry.url_auth( tool_shed_url ), pathspec=pathspec, params=params )
         tool_shed_accessible = True
     except Exception, e:
         tool_shed_accessible = False
-        log.warn( "The URL\n%s\nraised the exception:\n%s\n", url_join( tool_shed_url, pathspec=pathspec, params=params ), e )
+        log.warn( "The URL\n%s\nraised the exception:\n%s\n", util.build_url( tool_shed_url, pathspec=pathspec, params=params ), e )
     if tool_shed_accessible:
         if text:
             tool_dependencies_dict = encoding_util.tool_shed_decode( text )
@@ -339,34 +336,3 @@ def remove_protocol_and_user_from_clone_url( repository_clone_url ):
 def remove_protocol_from_tool_shed_url( tool_shed_url ):
     """Return a partial Tool Shed URL, eliminating the protocol if it exists."""
     return util.remove_protocol_from_url( tool_shed_url )
-
-
-def tool_shed_get( app, base_url, pathspec=None, params=None ):
-    """Make contact with the tool shed via the uri provided."""
-    registry = app.tool_shed_registry
-    # urllib2 auto-detects system proxies, when passed a Proxyhandler.
-    # Refer: https://docs.python.org/2/howto/urllib2.html#proxies
-    proxy = urllib2.ProxyHandler()
-    urlopener = urllib2.build_opener( proxy )
-    urllib2.install_opener( urlopener )
-    password_mgr = registry.password_manager_for_url( base_url )
-    if password_mgr is not None:
-        auth_handler = urllib2.HTTPBasicAuthHandler( password_mgr )
-        urlopener.add_handler( auth_handler )
-    full_url = url_join( base_url, pathspec=pathspec, params=params )
-    response = urlopener.open( full_url )
-    content = response.read()
-    response.close()
-    return content
-
-
-def url_join( base_url, pathspec=None, params=None ):
-    """Return a valid URL produced by appending a base URL and a set of request parameters."""
-    url = base_url.rstrip( '/' )
-    if pathspec is not None:
-        if not isinstance( pathspec, string_types ):
-            pathspec = '/'.join( pathspec )
-        url = '%s/%s' % ( url, pathspec )
-    if params is not None:
-        url = '%s?%s' % ( url, urllib.urlencode( params ) )
-    return url
diff --git a/lib/tool_shed/util/readme_util.py b/lib/tool_shed/util/readme_util.py
index a68f01f1036..82b919db440 100644
--- a/lib/tool_shed/util/readme_util.py
+++ b/lib/tool_shed/util/readme_util.py
@@ -7,7 +7,7 @@ from mako.template import Template
 
 import tool_shed.util.shed_util_common as suc
 from galaxy import web
-from galaxy.util import rst_to_html, unicodify
+from galaxy.util import rst_to_html, unicodify, url_get
 from tool_shed.util import basic_util, common_util, hg_util
 
 log = logging.getLogger( __name__ )
@@ -97,7 +97,7 @@ def get_readme_files_dict_for_display( app, tool_shed_url, repo_info_dict ):
     tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( app, tool_shed_url )
     params = dict( name=name, owner=repository_owner, changeset_revision=changeset_revision )
     pathspec = [ 'repository', 'get_readme_files' ]
-    raw_text = common_util.tool_shed_get( app, tool_shed_url, pathspec=pathspec, params=params )
+    raw_text = url_get( tool_shed_url, password_mgr=app.tool_shed_registry.url_auth( tool_shed_url ), pathspec=pathspec, params=params )
     readme_files_dict = json.loads( raw_text )
     return readme_files_dict
 
diff --git a/lib/tool_shed/util/shed_util_common.py b/lib/tool_shed/util/shed_util_common.py
index 9596585ec40..5c0fefa7e63 100644
--- a/lib/tool_shed/util/shed_util_common.py
+++ b/lib/tool_shed/util/shed_util_common.py
@@ -254,7 +254,7 @@ def generate_tool_shed_repository_install_dir( repository_clone_url, changeset_r
     tool_shed_url = items[ 0 ]
     repo_path = items[ 1 ]
     tool_shed_url = common_util.remove_port_from_tool_shed_url( tool_shed_url )
-    return common_util.url_join( tool_shed_url, pathspec=[ 'repos', repo_path, changeset_revision ] )
+    return '/'.join( [ tool_shed_url, 'repos', repo_path, changeset_revision ] )
 
 
 def get_absolute_path_to_file_in_repository( repo_files_dir, file_name ):
@@ -301,7 +301,7 @@ def get_ctx_rev( app, tool_shed_url, name, owner, changeset_revision ):
     tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( app, tool_shed_url )
     params = dict( name=name, owner=owner, changeset_revision=changeset_revision )
     pathspec = [ 'repository', 'get_ctx_rev' ]
-    ctx_rev = common_util.tool_shed_get( app, tool_shed_url, pathspec=pathspec, params=params )
+    ctx_rev = util.url_get( tool_shed_url, password_mgr=app.tool_shed_registry.url_auth( tool_shed_url ), pathspec=pathspec, params=params )
     return ctx_rev
 
 
@@ -369,7 +369,7 @@ def get_tool_dependency_definition_metadata_from_tool_shed( app, tool_shed_url,
     tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( app, tool_shed_url )
     params = dict( name=name, owner=owner )
     pathspec = [ 'repository', 'get_tool_dependency_definition_metadata' ]
-    metadata = common_util.tool_shed_get( app, tool_shed_url, pathspec=pathspec, params=params )
+    metadata = util.url_get( tool_shed_url, password_mgr=app.tool_shed_registry.url_auth( tool_shed_url ), pathspec=pathspec, params=params )
     return metadata
 
 
@@ -626,7 +626,7 @@ def get_repository_for_dependency_relationship( app, tool_shed, name, owner, cha
         tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( app, tool_shed )
         params = dict( name=name, owner=owner, changeset_revision=changeset_revision )
         pathspec = [ 'repository', 'next_installable_changeset_revision' ]
-        text = common_util.tool_shed_get( app, tool_shed_url, pathspec=pathspec, params=params )
+        text = util.url_get( tool_shed_url, password_mgr=app.tool_shed_registry.url_auth( tool_shed_url ), pathspec=pathspec, params=params )
         if text:
             repository = get_installed_repository( app=app,
                                                    tool_shed=tool_shed,
@@ -828,7 +828,7 @@ def get_repository_type_from_tool_shed( app, tool_shed_url, name, owner ):
     tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( app, tool_shed_url )
     params = dict( name=name, owner=owner )
     pathspec = [ 'repository', 'get_repository_type' ]
-    repository_type = common_util.tool_shed_get( app, tool_shed_url, pathspec=pathspec, params=params )
+    repository_type = util.url_get( tool_shed_url, password_mgr=app.tool_shed_registry.url_auth( tool_shed_url ), pathspec=pathspec, params=params )
     return repository_type
 
 
@@ -914,7 +914,7 @@ def get_tool_shed_status_for_installed_repository( app, repository ):
     params = dict( name=repository.name, owner=repository.owner, changeset_revision=repository.changeset_revision )
     pathspec = [ 'repository', 'status_for_installed_repository' ]
     try:
-        encoded_tool_shed_status_dict = common_util.tool_shed_get( app, tool_shed_url, pathspec=pathspec, params=params )
+        encoded_tool_shed_status_dict = util.url_get( tool_shed_url, password_mgr=app.tool_shed_registry.url_auth( tool_shed_url ), pathspec=pathspec, params=params )
         tool_shed_status_dict = encoding_util.tool_shed_decode( encoded_tool_shed_status_dict )
         return tool_shed_status_dict
     except HTTPError, e:
@@ -926,7 +926,7 @@ def get_tool_shed_status_for_installed_repository( app, repository ):
         params[ 'from_update_manager' ] = True
         try:
             # The value of text will be 'true' or 'false', depending upon whether there is an update available for the installed revision.
-            text = common_util.tool_shed_get( app, tool_shed_url, pathspec=pathspec, params=params )
+            text = util.url_get( tool_shed_url, password_mgr=app.tool_shed_registry.url_auth( tool_shed_url ), pathspec=pathspec, params=params )
             return dict( revision_update=text )
         except Exception, e:
             # The required tool shed may be unavailable, so default the revision_update value to 'false'.
@@ -1021,7 +1021,7 @@ def get_updated_changeset_revisions_from_tool_shed( app, tool_shed_url, name, ow
         raise Exception( message )
     params = dict( name=name, owner=owner, changeset_revision=changeset_revision )
     pathspec = [ 'repository', 'updated_changeset_revisions' ]
-    text = common_util.tool_shed_get( app, tool_shed_url, pathspec=pathspec, params=params )
+    text = util.url_get( tool_shed_url, password_mgr=app.tool_shed_registry.url_auth( tool_shed_url ), pathspec=pathspec, params=params )
     return text
 
 
@@ -1227,7 +1227,7 @@ def repository_was_previously_installed( app, tool_shed_url, repository_name, re
                    changeset_revision=changeset_revision,
                    from_tip=str( from_tip ) )
     pathspec = [ 'repository', 'previous_changeset_revisions' ]
-    text = common_util.tool_shed_get( app, tool_shed_url, pathspec=pathspec, params=params )
+    text = util.url_get( tool_shed_url, password_mgr=app.tool_shed_registry.url_auth( tool_shed_url ), pathspec=pathspec, params=params )
     if text:
         changeset_revisions = util.listify( text )
         for previous_changeset_revision in changeset_revisions: