Filter tool dependency installation to only those that were checked when installing them from the Manage tool dependencies page for an installed tool shed repository.

lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py

@@ -701,11 +701,11 @@ class AdminToolshed( AdminGalaxy ):
         installed_tool_dependencies_select_field = suc.build_tool_dependencies_select_field( trans,
                                                                                              tool_shed_repository=tool_shed_repository,
                                                                                              name='inst_td_ids',
-                                                                                             uninstalled=False )
+                                                                                             uninstalled_only=False )
         uninstalled_tool_dependencies_select_field = suc.build_tool_dependencies_select_field( trans,
                                                                                                tool_shed_repository=tool_shed_repository,
                                                                                                name='uninstalled_tool_dependency_ids',
-                                                                                               uninstalled=True )
+                                                                                               uninstalled_only=True )
         return trans.fill_template( '/admin/tool_shed_repository/manage_repository_tool_dependencies.mako',
                                     repository=tool_shed_repository,
                                     installed_tool_dependencies_select_field=installed_tool_dependencies_select_field,

lib/tool_shed/util/common_install_util.py

@@ -429,6 +429,10 @@ def handle_tool_dependencies( app, tool_shed_repository, tool_dependencies_confi
     will be installed in:
     ~/<app.config.tool_dependency_dir>/<package_name>/<package_version>/<repo_owner>/<repo_name>/<repo_installed_changeset_revision>
     """
+    # The received list of tool_dependencies are the database records for those dependencies defined in the received tool_dependencies_config
+    # that should be installed.  This allows for filtering out dependencies that have not been checked for installation on the 'Manage tool
+    # dependencies' page for an installed tool shed repository.
+    attr_tups_of_dependencies_for_install = [ ( td.name, td.version, td.type ) for td in tool_dependencies ]
     sa_session = app.model.context.current
     installed_tool_dependencies = []
     # Parse the tool_dependencies.xml config.
@@ -439,19 +443,43 @@ def handle_tool_dependencies( app, tool_shed_repository, tool_dependencies_confi
     fabric_version_checked = False
     for elem in root:
         if elem.tag == 'package':
-            # Only install the tool_dependency if it is not already installed.
+            # Only install the tool_dependency if it is not already installed and it is associated with a database record in the received
+            # tool_dependencies.
             package_name = elem.get( 'name', None )
             package_version = elem.get( 'version', None )
             if package_name and package_version:
-                for tool_dependency in tool_dependencies:
-                    if tool_dependency.name==package_name and tool_dependency.version==package_version:
-                        break
-                if tool_dependency.can_install:
+                attr_tup = ( package_name, package_version, 'package' )
+                try:
+                    index = attr_tups_of_dependencies_for_install.index( attr_tup )
+                except Exception, e:
+                    index = None
+                if index is not None:
+                    tool_dependency = tool_dependencies[ index ]
+                    if tool_dependency.can_install:
+                        try:
+                            tool_dependency = install_package( app, elem, tool_shed_repository, tool_dependencies=tool_dependencies )
+                        except Exception, e:
+                            error_message = "Error installing tool dependency %s version %s: %s" % ( str( package_name ), str( package_version ), str( e ) )
+                            log.exception( error_message )
+                            if tool_dependency:
+                                tool_dependency.status = app.model.ToolDependency.installation_status.ERROR
+                                tool_dependency.error_message = error_message
+                                sa_session.add( tool_dependency )
+                                sa_session.flush()
+                        if tool_dependency and tool_dependency.status in [ app.model.ToolDependency.installation_status.INSTALLED,
+                                                                           app.model.ToolDependency.installation_status.ERROR ]:
+                            installed_tool_dependencies.append( tool_dependency )
+        elif elem.tag == 'set_environment':
+            env_var_name = env_var_elem.get( 'name', None )
+            if env_var_name:
+                # Tool dependencies of type "set_environmnet" always have the version attribute set to None.
+                attr_tup = ( env_var_name, None, 'set_environment' )
+                if attr_tup in attr_tups_of_dependencies_for_install:
                     try:
-                        tool_dependency = install_package( app, elem, tool_shed_repository, tool_dependencies=tool_dependencies )
+                        tool_dependency = set_environment( app, elem, tool_shed_repository )
                     except Exception, e:
-                        error_message = "Error installing tool dependency %s version %s: %s" % ( str( package_name ), str( package_version ), str( e ) )
-                        log.exception( error_message )
+                        error_message = "Error setting environment for tool dependency: %s" % str( e )
+                        log.debug( error_message )
                         if tool_dependency:
                             tool_dependency.status = app.model.ToolDependency.installation_status.ERROR
                             tool_dependency.error_message = error_message
@@ -460,20 +488,6 @@ def handle_tool_dependencies( app, tool_shed_repository, tool_dependencies_confi
                     if tool_dependency and tool_dependency.status in [ app.model.ToolDependency.installation_status.INSTALLED,
                                                                        app.model.ToolDependency.installation_status.ERROR ]:
                         installed_tool_dependencies.append( tool_dependency )
-        elif elem.tag == 'set_environment':
-            try:
-                tool_dependency = set_environment( app, elem, tool_shed_repository )
-            except Exception, e:
-                error_message = "Error setting environment for tool dependency: %s" % str( e )
-                log.debug( error_message )
-                if tool_dependency:
-                    tool_dependency.status = app.model.ToolDependency.installation_status.ERROR
-                    tool_dependency.error_message = error_message
-                    sa_session.add( tool_dependency )
-                    sa_session.flush()
-            if tool_dependency and tool_dependency.status in [ app.model.ToolDependency.installation_status.INSTALLED,
-                                                               app.model.ToolDependency.installation_status.ERROR ]:
-                installed_tool_dependencies.append( tool_dependency )
     return installed_tool_dependencies
 
 def repository_dependency_needed_only_for_compiling_tool_dependency( repository, repository_dependency ):

lib/tool_shed/util/shed_util_common.py

@@ -144,13 +144,18 @@ def build_repository_ids_select_field( trans, name='repository_ids', multiple=Tr
             repositories_select_field.add_option( option_label, option_value )
     return repositories_select_field
 
-def build_tool_dependencies_select_field( trans, tool_shed_repository, name, multiple=True, display='checkboxes', uninstalled=False ):
+def build_tool_dependencies_select_field( trans, tool_shed_repository, name, multiple=True, display='checkboxes', uninstalled_only=False ):
     """Method called from Galaxy to generate the current list of tool dependency ids for an installed tool shed repository."""
     tool_dependencies_select_field = SelectField( name=name, multiple=multiple, display=display )
     for tool_dependency in tool_shed_repository.tool_dependencies:
-        if uninstalled and tool_dependency.status not in [ trans.model.ToolDependency.installation_status.NEVER_INSTALLED,
-                                                           trans.model.ToolDependency.installation_status.UNINSTALLED ]:
-            continue
+        if uninstalled_only:
+            if tool_dependency.status not in [ trans.model.ToolDependency.installation_status.NEVER_INSTALLED,
+                                               trans.model.ToolDependency.installation_status.UNINSTALLED ]:
+                continue
+        else:
+            if tool_dependency.status in [ trans.model.ToolDependency.installation_status.NEVER_INSTALLED,
+                                           trans.model.ToolDependency.installation_status.UNINSTALLED ]:
+                continue
         option_label = '%s version %s' % ( str( tool_dependency.name ), str( tool_dependency.version ) )
         option_value = trans.security.encode_id( tool_dependency.id )
         tool_dependencies_select_field.add_option( option_label, option_value )