Merge branch 'dev' of git://github.com/galaxyproject/galaxy into repo…

…_queue_sharing

doc/source/admin/chat.rst

@@ -115,7 +115,7 @@ This service does not:
 
 - enforce rate-limiting of messages
 - run any sort of text/obscenity filtering rules
-- prevent user spoofing is the user is an administrator and impersonating
+- prevent user spoofing if the user is an administrator and impersonating
   another user
 
 Keeping the Chat Server Running

doc/source/admin/conda_faq.rst

@@ -274,7 +274,7 @@ install new tools, even if ``conda_auto_install`` is disabled.
 
 More improvements to the UI will be coming in future releases. To see if Galaxy
 has created a Trinity environment for you have a look at folder under
-``<tool_dependency_dir>/_conda/envs/``.
+``<tool_dependency_dir>/_conda/envs/``(or ``<conda_prefix>/envs`` if you have changed `conda_prefix` in your galaxy.ini file).
 
 
 12. Can I mix traditional Galaxy packages and Conda packages?
@@ -314,7 +314,7 @@ following in your galaxy log files:
 
 In rare cases Conda may not have been properly installed by Galaxy.
 A symptom for this is if there is no activate script in
-``conda_prefix/bin`` folder. In that case you can delete the ``conda_prefix`` folder
+``<conda_prefix>/bin`` folder. In that case you can delete the ``conda_prefix`` folder
 and restart Galaxy, which will again attempt to install Conda.
 
 If this does not solve your problem or you have any trouble following

lib/galaxy/tools/deps/conda_util.py

@@ -31,9 +31,9 @@
 
 def conda_link():
     if IS_OS_X:
-        url = "https://repo.continuum.io/miniconda/Miniconda-latest-MacOSX-x86_64.sh"
+        url = "https://repo.continuum.io/miniconda/Miniconda2-4.0.5-MacOSX-x86_64.sh"
     else:
-        url = "https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh"
+        url = "https://repo.continuum.io/miniconda/Miniconda2-4.0.5-Linux-x86_64.sh"
     return url
 
 

lib/galaxy/tools/toolbox/base.py

@@ -392,6 +392,11 @@ def get_tool( self, tool_id, tool_version=None, get_all_versions=False, exact=Fa
                     return self._tool_versions_by_id[ tool_id ][ tool_version ]
                 # tool_id exactly matches an available tool by id (which is 'old' tool_id or guid)
                 return self._tools_by_id[ tool_id ]
+            elif exact:
+                # We're looking for an exact match, so we skip lineage and
+                # versionless mapping, though we may want to check duplicate
+                # toolsheds
+                continue
             # exact tool id match not found, or all versions requested, search for other options, e.g. migrated tools or different versions
             rval = []
             tool_lineage = self._lineage_map.get( tool_id )

lib/galaxy/web/framework/webapp.py

@@ -660,7 +660,7 @@ def handle_user_login( self, user ):
                     users_last_session.current_history.deleted):
                 history = users_last_session.current_history
             elif not history:
-                history = self.get_history( create=True )
+                history = self.get_history( create=True, most_recent=True )
             if history not in self.galaxy_session.histories:
                 self.galaxy_session.add_history( history )
             if history.user is None:
@@ -708,17 +708,20 @@ def get_galaxy_session( self ):
         """
         return self.galaxy_session
 
-    def get_history( self, create=False ):
+    def get_history( self, create=False, most_recent=False ):
         """
-        Load the current history, creating a new one only if there is not
-        current history and we're told to create.
+        Load the current history.
+            - If that isn't available, we find the most recently updated history.
+            - If *that* isn't available, we get or create the default history.
         Transactions will not always have an active history (API requests), so
         None is a valid response.
         """
         history = None
         if self.galaxy_session:
             if hasattr( self.galaxy_session, 'current_history' ):
                 history = self.galaxy_session.current_history
+        if not history and most_recent:
+            history = self.get_most_recent_history()
         if not history and util.string_as_bool( create ):
             history = self.get_or_create_default_history()
         return history
@@ -764,6 +767,23 @@ def get_or_create_default_history( self ):
 
         return history
 
+    def get_most_recent_history( self ):
+        """
+        Gets the most recently updated history.
+        """
+        # There must be a user to fetch histories, and without a user we have
+        # no recent history.
+        if not self.galaxy_session.user:
+            return None
+        try:
+            recent_history = self.sa_session.query( self.app.model.History ).filter_by(
+                user=self.galaxy_session.user,
+                deleted=False ).order_by(self.app.model.History.update_time.desc()).first()
+        except NoResultFound:
+            return None
+        self.set_history(recent_history)
+        return recent_history
+
     def new_history( self, name=None ):
         """
         Create a new history and associate it with the current session and

lib/galaxy/webapps/galaxy/controllers/admin.py

@@ -445,7 +445,7 @@ def get_value( self, trans, grid, tool_version ):
             toolbox = trans.app.toolbox
             if toolbox.has_tool( tool_version.tool_id, exact=True ):
                 link = url_for( controller='tool_runner', tool_id=tool_version.tool_id )
-                link_str = '<a href="%s">' % link
+                link_str = '<a target="_blank" href="%s">' % link
                 return '<div class="count-box state-color-ok">%s%s</a></div>' % ( link_str, tool_version.tool_id )
             return tool_version.tool_id
 
@@ -455,8 +455,8 @@ def get_value( self, trans, grid, tool_version ):
             toolbox = trans.app.toolbox
             for tool_id in tool_version.get_version_ids( trans.app ):
                 if toolbox.has_tool( tool_id, exact=True ):
-                    link = url_for( controller='tool_runner', tool_id=tool_version.tool_id )
-                    link_str = '<a href="%s">' % link
+                    link = url_for( controller='tool_runner', tool_id=tool_id )
+                    link_str = '<a target="_blank" href="%s">' % link
                     tool_ids_str += '<div class="count-box state-color-ok">%s%s</a></div><br/>' % ( link_str, tool_id )
                 else:
                     tool_ids_str += '%s<br/>' % tool_id

lib/galaxy/webapps/galaxy/controllers/history.py

@@ -487,7 +487,7 @@ def as_xml( self, trans, id=None, show_deleted=None, show_hidden=None ):
             history = self.history_manager.get_accessible( self.decode_id( id ), trans.user,
                 current_history=trans.history )
         else:
-            history = trans.get_history( create=True )
+            history = trans.get_history( most_recent=True, create=True )
 
         trans.response.set_content_type( 'text/xml' )
         return trans.fill_template_mako(
@@ -1351,7 +1351,7 @@ def current_history_json( self, trans ):
         """Return the current user's current history in a serialized, dictionary form."""
         # Prevent IE11 from caching this
         trans.response.headers[ 'Cache-Control' ] = ["max-age=0", "no-cache", "no-store"]
-        history = trans.get_history( create=True )
+        history = trans.get_history( most_recent=True, create=True )
         return self.history_data( trans, history )
 
     @web.json

lib/galaxy/webapps/galaxy/controllers/visualization.py

@@ -955,7 +955,7 @@ def sweepster( self, trans, id=None, hda_ldda=None, dataset_id=None, regions=Non
         """
         regions = regions or '{}'
         # Need to create history if necessary in order to create tool form.
-        trans.get_history( create=True )
+        trans.get_history( most_recent=True, create=True )
 
         if id:
             # Loading a shared visualization.

templates/webapps/galaxy/workflow/display.mako

@@ -90,7 +90,7 @@
     <%
         # HACK: Rendering workflow steps requires that trans have a history; however, if its user's first visit to Galaxy is here, he won't have a history
         # and an error will occur. To prevent this error, make sure user has a history. 
-        trans.get_history( create=True ) 
+        trans.get_history( most_recent=True, create=True )
     %>
     <table class="annotated-item">
         <tr><th>Step</th><th class="annotation">Annotation</th></tr>