[galaxy-commits] commit/galaxy-central: greg: Use a template for managing tool dependencies for a specified installed tool shed repository instead of a grid.

19 Jun 2013

1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/d842d50a6ed3/
Changeset:   d842d50a6ed3
User:        greg
Date:        2013-06-19 22:55:28
Summary:     Use a template for managing tool dependencies for a specified installed tool shed repository instead of a grid.
Affected #:  8 files

diff -r d4d1d086e50d70eecb13fa0b61f738f09f8eefdd -r d842d50a6ed3241b3b888c2b6324fc59e9fa3134 lib/galaxy/model/__init__.py

--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -3569,7 +3569,7 @@
     def repository_dependencies_being_installed( self ):
         required_repositories_being_installed = []
         for required_repository in self.repository_dependencies:
-            if tool_dependency.status == ToolDependency.installation_status.INSTALLING:
+            if required_repository.status == self.installation_status.INSTALLING:
                 required_repositories_being_installed.append( required_repository )
         return required_repositories_being_installed
     @property

diff -r d4d1d086e50d70eecb13fa0b61f738f09f8eefdd -r d842d50a6ed3241b3b888c2b6324fc59e9fa3134 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -509,7 +509,7 @@
                 message = 'All of the selected tool dependencies are already installed.'
                 status = 'error'
                 return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
-                                                                  action='manage_tool_dependencies',
+                                                                  action='manage_repository_tool_dependencies',
                                                                   tool_dependency_ids=tool_dependency_ids,
                                                                   status=status,
                                                                   message=message ) )
@@ -546,62 +546,6 @@
 
     @web.expose
     @web.require_admin
-    def manage_repository( self, trans, **kwd ):
-        message = kwd.get( 'message', ''  )
-        status = kwd.get( 'status', 'done' )
-        repository_id = kwd[ 'id' ]
-        operation = kwd.get( 'operation', None )
-        repository = suc.get_installed_tool_shed_repository( trans, repository_id )
-        if not repository:
-            return trans.show_error_message( 'Invalid repository specified.' )
-        tool_shed_url = suc.get_url_from_tool_shed( trans.app, repository.tool_shed )
-        if repository.status in [ trans.model.ToolShedRepository.installation_status.CLONING ]:
-            tool_shed_repository_ids = [ repository_id ]
-            return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
-                                                              action='monitor_repository_installation',
-                                                              tool_shed_repository_ids=tool_shed_repository_ids ) )
-        if repository.can_install and operation == 'install':
-            # Send a request to the tool shed to install the repository.
-            url = suc.url_join( tool_shed_url,
-                                'repository/install_repositories_by_revision?name=%s&owner=%s&changeset_revisions=%s&galaxy_url=%s' % \
-                                ( repository.name, repository.owner, repository.installed_changeset_revision, ( web.url_for( '/', qualified=True ) ) ) )
-            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 )
-        if relative_install_dir:
-            repo_files_dir = os.path.abspath( os.path.join( tool_path, relative_install_dir, repository.name ) )
-        else:
-            repo_files_dir = None
-        if repository.in_error_state:
-            message = "This repository is not installed correctly (see the <b>Repository installation error</b> below).  Choose "
-            message += "<b>Reset to install</b> from the <b>Repository Actions</b> menu, correct problems if necessary and try "
-            message += "installing the repository again."
-            status = "error"
-        elif repository.can_install:
-            message = "This repository is not installed.  You can install it by choosing  <b>Install</b> from the <b>Repository Actions</b> menu."
-            status = "error"
-        elif kwd.get( 'edit_repository_button', False ):
-            if description != repository.description:
-                repository.description = description
-                trans.sa_session.add( repository )
-                trans.sa_session.flush()
-            message = "The repository information has been updated."
-        containers_dict = metadata_util.populate_containers_dict_from_repository_metadata( trans=trans,
-                                                                                           tool_shed_url=tool_shed_url,
-                                                                                           tool_path=tool_path,
-                                                                                           repository=repository,
-                                                                                           reinstalling=False,
-                                                                                           required_repo_info_dicts=None )
-        return trans.fill_template( '/admin/tool_shed_repository/manage_repository.mako',
-                                    repository=repository,
-                                    description=description,
-                                    repo_files_dir=repo_files_dir,
-                                    containers_dict=containers_dict,
-                                    message=message,
-                                    status=status )
-
-    @web.expose
-    @web.require_admin
     def manage_repositories( self, trans, **kwd ):
         message = kwd.get( 'message', ''  )
         status = kwd.get( 'status', 'done' )
@@ -676,35 +620,69 @@
 
     @web.expose
     @web.require_admin
-    def manage_tool_dependencies( self, trans, **kwd ):
+    def manage_repository( self, trans, **kwd ):
+        message = kwd.get( 'message', ''  )
+        status = kwd.get( 'status', 'done' )
+        repository_id = kwd[ 'id' ]
+        operation = kwd.get( 'operation', None )
+        repository = suc.get_installed_tool_shed_repository( trans, repository_id )
+        if not repository:
+            return trans.show_error_message( 'Invalid repository specified.' )
+        tool_shed_url = suc.get_url_from_tool_shed( trans.app, repository.tool_shed )
+        if repository.status in [ trans.model.ToolShedRepository.installation_status.CLONING ]:
+            tool_shed_repository_ids = [ repository_id ]
+            return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
+                                                              action='monitor_repository_installation',
+                                                              tool_shed_repository_ids=tool_shed_repository_ids ) )
+        if repository.can_install and operation == 'install':
+            # Send a request to the tool shed to install the repository.
+            url = suc.url_join( tool_shed_url,
+                                'repository/install_repositories_by_revision?name=%s&owner=%s&changeset_revisions=%s&galaxy_url=%s' % \
+                                ( repository.name, repository.owner, repository.installed_changeset_revision, ( web.url_for( '/', qualified=True ) ) ) )
+            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 )
+        if relative_install_dir:
+            repo_files_dir = os.path.abspath( os.path.join( tool_path, relative_install_dir, repository.name ) )
+        else:
+            repo_files_dir = None
+        if repository.in_error_state:
+            message = "This repository is not installed correctly (see the <b>Repository installation error</b> below).  Choose "
+            message += "<b>Reset to install</b> from the <b>Repository Actions</b> menu, correct problems if necessary and try "
+            message += "installing the repository again."
+            status = "error"
+        elif repository.can_install:
+            message = "This repository is not installed.  You can install it by choosing  <b>Install</b> from the <b>Repository Actions</b> menu."
+            status = "error"
+        elif kwd.get( 'edit_repository_button', False ):
+            if description != repository.description:
+                repository.description = description
+                trans.sa_session.add( repository )
+                trans.sa_session.flush()
+            message = "The repository information has been updated."
+        containers_dict = metadata_util.populate_containers_dict_from_repository_metadata( trans=trans,
+                                                                                           tool_shed_url=tool_shed_url,
+                                                                                           tool_path=tool_path,
+                                                                                           repository=repository,
+                                                                                           reinstalling=False,
+                                                                                           required_repo_info_dicts=None )
+        return trans.fill_template( '/admin/tool_shed_repository/manage_repository.mako',
+                                    repository=repository,
+                                    description=description,
+                                    repo_files_dir=repo_files_dir,
+                                    containers_dict=containers_dict,
+                                    message=message,
+                                    status=status )
+
+    @web.expose
+    @web.require_admin
+    def manage_repository_tool_dependencies( self, trans, **kwd ):
         message = kwd.get( 'message', ''  )
         status = kwd.get( 'status', 'done' )
         tool_dependency_ids = tool_dependency_util.get_tool_dependency_ids( as_string=False, **kwd )
         # We need a tool_shed_repository, so get it from one of the tool_dependencies.
         tool_dependency = tool_dependency_util.get_tool_dependency( trans, tool_dependency_ids[ 0 ] )
         tool_shed_repository = tool_dependency.tool_shed_repository
-        self.tool_dependency_grid.title = "Tool shed repository '%s' tool dependencies"  % tool_shed_repository.name
-        self.tool_dependency_grid.global_actions = \
-            [ grids.GridAction( label='Manage repository', 
-                                url_args=dict( controller='admin_toolshed', 
-                                               action='manage_repository', 
-                                               id=trans.security.encode_id( tool_shed_repository.id ) ) ),
-              grids.GridAction( label='Browse repository', 
-                                url_args=dict( controller='admin_toolshed', 
-                                               action='browse_repository', 
-                                               id=trans.security.encode_id( tool_shed_repository.id ) ) ),
-              grids.GridAction( label='Get repository updates', 
-                                url_args=dict( controller='admin_toolshed', 
-                                               action='check_for_updates', 
-                                               id=trans.security.encode_id( tool_shed_repository.id ) ) ),
-              grids.GridAction( label='Set tool versions', 
-                                url_args=dict( controller='admin_toolshed', 
-                                               action='set_tool_versions', 
-                                               id=trans.security.encode_id( tool_shed_repository.id ) ) ),
-              grids.GridAction( label='Deactivate or uninstall repository', 
-                                url_args=dict( controller='admin_toolshed', 
-                                               action='deactivate_or_uninstall_repository', 
-                                               id=trans.security.encode_id( tool_shed_repository.id ) ) ) ]
         if 'operation' in kwd:
             operation = kwd[ 'operation' ].lower()
             if not tool_dependency_ids:
@@ -713,7 +691,7 @@
                 kwd[ 'status' ] = 'error'
                 del kwd[ 'operation' ]
                 return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
-                                                                  action='manage_tool_dependencies',
+                                                                  action='manage_installed_tool_dependencies',
                                                                   **kwd ) )
             if operation == 'browse':
                 return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
@@ -750,8 +728,74 @@
                         message = 'Set the value of your <b>tool_dependency_dir</b> setting in your Galaxy config file (universe_wsgi.ini) '
                         message += ' and restart your Galaxy server to install tool dependencies.'
                         kwd[ 'message' ] = message
-                        kwd[ 'status' ] = 'error'  
-        return self.tool_dependency_grid( trans, **kwd )
+                        kwd[ 'status' ] = 'error'
+        installed_tool_dependencies_select_field = suc.build_tool_dependencies_select_field( trans,
+                                                                                             tool_shed_repository=tool_shed_repository,
+                                                                                             name='tool_dependency_ids',
+                                                                                             uninstalled=False )
+        uninstalled_tool_dependencies_select_field = suc.build_tool_dependencies_select_field( trans,
+                                                                                               tool_shed_repository=tool_shed_repository,
+                                                                                               name='tool_dependency_ids',
+                                                                                               uninstalled=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,
+                                    uninstalled_tool_dependencies_select_field=uninstalled_tool_dependencies_select_field,
+                                    message=message,
+                                    status=status )
+
+    @web.expose
+    @web.require_admin
+    def manage_tool_dependencies( self, trans, **kwd ):
+        # This method is called when tool dependencies are being installed.  See the related manage_repository_tool-dependencies
+        # method for managing the tool dependencies for a specified installed tool shed repository.
+        message = kwd.get( 'message', ''  )
+        status = kwd.get( 'status', 'done' )
+        tool_dependency_ids = tool_dependency_util.get_tool_dependency_ids( as_string=False, **kwd )
+        # We need a tool_shed_repository, so get it from one of the tool_dependencies.
+        tool_dependency = tool_dependency_util.get_tool_dependency( trans, tool_dependency_ids[ 0 ] )
+        tool_shed_repository = tool_dependency.tool_shed_repository
+        self.tool_dependency_grid.title = "Tool shed repository '%s' tool dependencies"  % tool_shed_repository.name
+        if 'operation' in kwd:
+            operation = kwd[ 'operation' ].lower()
+            if not tool_dependency_ids:
+                message = 'Select at least 1 tool dependency to %s.' % operation
+                kwd[ 'message' ] = message
+                kwd[ 'status' ] = 'error'
+                del kwd[ 'operation' ]
+                return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
+                                                                  action='manage_tool_dependencies',
+                                                                  **kwd ) )
+            if operation == 'browse':
+                return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
+                                                                  action='browse_tool_dependency',
+                                                                  **kwd ) )
+            elif operation == "install":
+                if trans.app.config.tool_dependency_dir:
+                    tool_dependencies_for_installation = []
+                    for tool_dependency_id in tool_dependency_ids:
+                        tool_dependency = tool_dependency_util.get_tool_dependency( trans, tool_dependency_id )
+                        if tool_dependency.status in [ trans.model.ToolDependency.installation_status.NEVER_INSTALLED,
+                                                       trans.model.ToolDependency.installation_status.UNINSTALLED ]:
+                            tool_dependencies_for_installation.append( tool_dependency )
+                    if tool_dependencies_for_installation:
+                        self.initiate_tool_dependency_installation( trans, tool_dependencies_for_installation )
+                    else:
+                        kwd[ 'message' ] = 'All selected tool dependencies are already installed.'
+                        kwd[ 'status' ] = 'error'
+                else:
+                        message = 'Set the value of your <b>tool_dependency_dir</b> setting in your Galaxy config file (universe_wsgi.ini) '
+                        message += ' and restart your Galaxy server to install tool dependencies.'
+                        kwd[ 'message' ] = message
+                        kwd[ 'status' ] = 'error'
+        # Redirect if no tool dependencies are in the process of being installed.
+        if tool_shed_repository.tool_dependencies_being_installed:
+            return self.tool_dependency_grid( trans, **kwd )
+        return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
+                                                          action='manage_repository_tool_dependencies',
+                                                          tool_dependency_ids=tool_dependency_ids,
+                                                          message=message,
+                                                          status=status ) )
 
     @web.expose
     @web.require_admin
@@ -1449,7 +1493,7 @@
                 message = "These tool dependencies have been uninstalled: %s" % ','.join( td.name for td in tool_dependencies_for_uninstallation )
             td_ids = [ trans.security.encode_id( td.id ) for td in tool_shed_repository.tool_dependencies ]
             return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
-                                                              action='manage_tool_dependencies',
+                                                              action='manage_repository_tool_dependencies',
                                                               tool_dependency_ids=td_ids,
                                                               status=status,
                                                               message=message ) )

diff -r d4d1d086e50d70eecb13fa0b61f738f09f8eefdd -r d842d50a6ed3241b3b888c2b6324fc59e9fa3134 lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
--- a/lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
+++ b/lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
@@ -319,11 +319,11 @@
     use_paging = False
     columns = [
         NameColumn( "Name",
-                    link=( lambda item: iff( item.status in \
-                                             [ model.ToolDependency.installation_status.NEVER_INSTALLED,
-                                               model.ToolDependency.installation_status.INSTALLING,
-                                               model.ToolDependency.installation_status.UNINSTALLED ], \
-                                             None, dict( action="manage_tool_dependencies", operation='browse', id=item.id ) ) ),
+                    link=( lambda item: iff( item.status in [ model.ToolDependency.installation_status.NEVER_INSTALLED,
+                                                              model.ToolDependency.installation_status.INSTALLING,
+                                                              model.ToolDependency.installation_status.UNINSTALLED ],
+                                             None,
+                                             dict( action="manage_tool_dependencies", operation='browse', id=item.id ) ) ),
                     filterable="advanced" ),
         VersionColumn( "Version",
                        filterable="advanced" ),
@@ -332,17 +332,6 @@
         StatusColumn( "Installation Status",
                       filterable="advanced" ),
     ]
-    operations = [
-        grids.GridOperation( "Install",
-                             allow_multiple=True,
-                             condition=( lambda item: item.status in [ model.ToolDependency.installation_status.NEVER_INSTALLED,
-                                                                       model.ToolDependency.installation_status.UNINSTALLED ] ) ),
-        grids.GridOperation( "Uninstall",
-                             allow_multiple=True,
-                             allow_popup=False,
-                             condition=( lambda item: item.status in [ model.ToolDependency.installation_status.INSTALLED,
-                                                                       model.ToolDependency.installation_status.ERROR ] ) )
-    ]
 
     def build_initial_query( self, trans, **kwd ):
         tool_dependency_ids = tool_dependency_util.get_tool_dependency_ids( as_string=False, **kwd )

diff -r d4d1d086e50d70eecb13fa0b61f738f09f8eefdd -r d842d50a6ed3241b3b888c2b6324fc59e9fa3134 lib/tool_shed/util/shed_util_common.py
--- a/lib/tool_shed/util/shed_util_common.py
+++ b/lib/tool_shed/util/shed_util_common.py
@@ -135,6 +135,17 @@
             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 ):
+    """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 != 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 )
+    return tool_dependencies_select_field
+
 def changeset_is_malicious( trans, id, changeset_revision, **kwd ):
     """Check the malicious flag in repository metadata for a specified change set"""
     repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision )

diff -r d4d1d086e50d70eecb13fa0b61f738f09f8eefdd -r d842d50a6ed3241b3b888c2b6324fc59e9fa3134 lib/tool_shed/util/workflow_util.py
--- a/lib/tool_shed/util/workflow_util.py
+++ b/lib/tool_shed/util/workflow_util.py
@@ -385,13 +385,6 @@
             workflow.has_errors = True
         # Stick this in the step temporarily.
         step.temp_input_connections = step_dict[ 'input_connections' ]
-
-        # This should be considered a *temporary* hack.
-        # Usually we'd use the UsesAnnotation mixin, but
-        # that's not possible here. This entire module
-        # needs to die and get replaced with the regular
-        # galaxy/workflow methods.
-        # See WORKFLOW_REFACTOR below.
         annotation = step_dict.get( 'annotation', '')
         if annotation:
             annotation = sanitize_html( annotation, 'utf-8', 'text/html' )
@@ -405,8 +398,6 @@
             trans.model.PostJobAction( pja_dict[ 'action_type' ],
                                  step, pja_dict[ 'output_name' ],
                                  pja_dict[ 'action_arguments' ] )
-        # End temporary hack
-
         steps.append( step )
         steps_by_external_id[ step_dict[ 'id' ] ] = step
     # Second pass to deal with connections between steps.
@@ -444,18 +435,12 @@
     workflow.stored_workflow = stored
     stored.latest_workflow = workflow
     stored.user = trans.user
-
-    # One more temporary hack like above to support workflow level annotations.
-    # Same caveats.
-    # WORKFLOW_REFACTOR
     if workflow_dict and workflow_dict.get('annotation',''):
         annotation = sanitize_html( workflow_dict['annotation'], 'utf-8', 'text/html' )
         new_annotation = trans.model.StoredWorkflowAnnotationAssociation()
         new_annotation.annotation = annotation
         new_annotation.user = trans.user
         stored.annotations.append(new_annotation)
-    # End temporary hack
-
     trans.sa_session.add( stored )
     trans.sa_session.flush()
     # Add a new entry to the Workflows menu.

diff -r d4d1d086e50d70eecb13fa0b61f738f09f8eefdd -r d842d50a6ed3241b3b888c2b6324fc59e9fa3134 templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako
--- /dev/null
+++ b/templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako
@@ -0,0 +1,104 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+<%namespace file="/admin/tool_shed_repository/repository_actions_menu.mako" import="*" />
+<%namespace file="/webapps/tool_shed/common/common.mako" import="common_misc_javascripts" />
+
+<%def name="stylesheets()">
+    ${parent.stylesheets()}
+    ${h.css( "library" )}
+</%def>
+
+<%def name="javascripts()">
+    ${parent.javascripts()}
+    ${common_misc_javascripts()}
+</%def>
+
+${render_galaxy_repository_actions( repository )}
+
+%if message:
+    ${render_msg( message, status )}
+%endif
+
+<div class="toolForm">
+    <div class="toolFormTitle">Tool shed repository '${repository.name}' tool dependencies</div>
+        <%
+            can_install = False
+            can_uninstall = False
+        %>
+        <br/><br/>
+        <table class="grid">
+            <tr><th  bgcolor="#D8D8D8">Name</th><th  bgcolor="#D8D8D8">Version</th><th  bgcolor="#D8D8D8">Type</th><th bgcolor="#D8D8D8">Status</th><th bgcolor="#D8D8D8">Error</th></tr>
+            %for tool_dependency in repository.tool_dependencies:
+                <%
+                    if tool_dependency.error_message:
+                        error_message = tool_dependency.error_message
+                    else:
+                        error_message = ''
+                    if not can_install:
+                        if tool_dependency.status not in [ trans.model.ToolDependency.installation_status.INSTALLED ]:
+                            can_install = True
+                    if not can_uninstall:
+                        if tool_dependency.status not in [ trans.model.ToolDependency.installation_status.UNINSTALLED ]:
+                            can_uninstall = True
+                %>
+                <tr>
+                    <td>
+                        %if tool_dependency.status not in [ trans.model.ToolDependency.installation_status.UNINSTALLED ]:
+                            <a target="galaxy_main" href="${h.url_for( controller='admin_toolshed', action='manage_repository_tool_dependencies', operation='browse', id=trans.security.encode_id( tool_dependency.id ) )}">
+                                ${tool_dependency.name}
+                            </a>
+                        %else:
+                            ${tool_dependency.name}
+                        %endif
+                    </td>
+                    <td>${tool_dependency.version}</td>
+                    <td>${tool_dependency.type}</td>
+                    <td>${tool_dependency.status}</td>
+                    <td>${error_message}</td>
+                </tr>
+            %endfor
+        </table>
+        %if can_install:
+            <br/>
+            <form name="install_tool_dependencies" id="install_tool_dependencies" action="${h.url_for( controller='admin_toolshed', action='manage_tool_dependencies', operation='install' )}" method="post" >
+                <div class="form-row">
+                    Check each tool dependency that you want to install and click <b>Install</b>.
+                </div>
+                <div style="clear: both"></div>
+                <div class="form-row">
+                    <input type="checkbox" id="checkAll" name="select_all_uninstalled_tool_dependencies_checkbox" value="true" onclick="checkAllFields('tool_dependency_ids');"/><input type="hidden" name="select_all_uninstalled_tool_dependencies_checkbox" value="true"/><b>Select/unselect all tool dependencies</b>
+                </div>
+                <div style="clear: both"></div>
+                <div class="form-row">
+                    ${uninstalled_tool_dependencies_select_field.get_html()}
+                </div>
+                <div style="clear: both"></div>
+                <div class="form-row">
+                    <input type="submit" name="install_button" value="Install"/></td>
+                </div>
+            </form>
+            <br/>
+        %endif
+        %if can_uninstall:
+            <br/>
+            <form name="uninstall_tool_dependencies" id="uninstall_tool_dependencies" action="${h.url_for( controller='admin_toolshed', action='manage_repository_tool_dependencies', operation='uninstall' )}" method="post" >
+                <div class="form-row">
+                    Check each tool dependency that you want to uninstall and click <b>Uninstall</b>.
+                </div>
+                <div style="clear: both"></div>
+                <div class="form-row">
+                    <input type="checkbox" id="checkAll" name="select_all_installed_tool_dependencies_checkbox" value="true" onclick="checkAllFields('tool_dependency_ids');"/><input type="hidden" name="select_all_installed_tool_dependencies_checkbox" value="true"/><b>Select/unselect all tool dependencies</b>
+                </div>
+                <div style="clear: both"></div>
+                <div class="form-row">
+                    ${installed_tool_dependencies_select_field.get_html()}
+                </div>
+                <div style="clear: both"></div>
+                <div class="form-row">
+                    <input type="submit" name="uninstall_button" value="Uninstall"/></td>
+                </div>
+            </form>
+            <br/>
+        %endif
+    </div>
+</div>

diff -r d4d1d086e50d70eecb13fa0b61f738f09f8eefdd -r d842d50a6ed3241b3b888c2b6324fc59e9fa3134 templates/admin/tool_shed_repository/repository_actions_menu.mako
--- a/templates/admin/tool_shed_repository/repository_actions_menu.mako
+++ b/templates/admin/tool_shed_repository/repository_actions_menu.mako
@@ -31,10 +31,10 @@
                     <a class="action-button" target="galaxy_main" href="${h.url_for( controller='admin_toolshed', action='set_tool_versions', id=trans.security.encode_id( repository.id ) )}">Set tool versions</a>
                 %endif
                 %if tool_dependency_ids:
-                    <a class="action-button" target="galaxy_main" href="${h.url_for( controller='admin_toolshed', action='manage_tool_dependencies', tool_dependency_ids=tool_dependency_ids )}">Manage tool dependencies</a>
+                    <a class="action-button" target="galaxy_main" href="${h.url_for( controller='admin_toolshed', action='manage_repository_tool_dependencies', tool_dependency_ids=tool_dependency_ids )}">Manage tool dependencies</a>
                 %endif
                 <a class="action-button" target="galaxy_main" href="${h.url_for( controller='admin_toolshed', action='deactivate_or_uninstall_repository', id=trans.security.encode_id( repository.id ) )}">Deactivate or uninstall repository</a>
             %endif
         </div></ul>
-</%def>
\ No newline at end of file
+</%def>

diff -r d4d1d086e50d70eecb13fa0b61f738f09f8eefdd -r d842d50a6ed3241b3b888c2b6324fc59e9fa3134 templates/webapps/tool_shed/repository/common.mako
--- a/templates/webapps/tool_shed/repository/common.mako
+++ b/templates/webapps/tool_shed/repository/common.mako
@@ -867,7 +867,7 @@
                         ${tool_dependency.name | h}
                     </a>
                 %elif tool_dependency.installation_status != 'Installed':
-                    <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='manage_tool_dependencies', id=trans.security.encode_id( tool_dependency.tool_dependency_id ) )}">
+                    <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='manage_repository_tool_dependencies', id=trans.security.encode_id( tool_dependency.tool_dependency_id ) )}">
                         ${tool_dependency.name}
                     </a>
                 %else:

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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[galaxy-commits] commit/galaxy-central: greg: Use a template for managing tool dependencies for a specified installed tool shed repository instead of a grid.

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