Add install resolver dependency button

and add install_resolver_dependency to ToolShedRepositoriesController

Author: mvdbeek

lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py

@@ -246,6 +246,7 @@ def install( self, trans, **kwd ):
         POST /api/tool_shed_repositories/install
         Initiate the installation of a repository.
 
+        :param install_resolver_dependencies: True to install resolvable dependencies.
         :param install_tool_dependencies: True to install tool dependencies.
         :param install_repository_dependencies: True to install repository dependencies.
         :param tool_panel_section_id: The unique identifier for an existing tool panel section
@@ -263,6 +264,7 @@ def install( self, trans, **kwd ):
         params[ 'tool_panel_section_id' ] = kwd.get( 'tool_panel_section_id', None )
         params[ 'new_tool_panel_section_label' ] = kwd.get( 'new_tool_panel_section', None )
         params[ 'tool_panel_section_mapping' ] = json.loads( kwd.get( 'tool_panel_section', '{}' ) )
+        params[ 'install_resolver_dependencies' ] = util.asbool( kwd.get( 'install_resolver_dependencies', False ) )
         params[ 'install_tool_dependencies' ] = util.asbool( kwd.get( 'install_tool_dependencies', False ) )
         params[ 'install_repository_dependencies' ] = util.asbool( kwd.get( 'install_repository_dependencies', False ) )
         params[ 'shed_tool_conf' ] = kwd.get( 'shed_tool_conf', None )
@@ -394,6 +396,7 @@ def install_repository_revisions( self, trans, payload, **kwd ):
         # TODO: we may want to enhance this method to allow for each of the following to be associated with each repository instead of
         # forcing all repositories to use the same settings.
         install_repository_dependencies = payload.get( 'install_repository_dependencies', False )
+        install_resolver_dependencies = payload.get( 'install_resolver_dependencies', False )
         install_tool_dependencies = payload.get( 'install_tool_dependencies', False )
         new_tool_panel_section_label = payload.get( 'new_tool_panel_section_label', '' )
         shed_tool_conf = payload.get( 'shed_tool_conf', None )
@@ -407,6 +410,7 @@ def install_repository_revisions( self, trans, payload, **kwd ):
                                     new_tool_panel_section_label=new_tool_panel_section_label,
                                     tool_panel_section_id=tool_panel_section_id,
                                     install_repository_dependencies=install_repository_dependencies,
+                                    install_resolver_dependencies=install_resolver_dependencies,
                                     install_tool_dependencies=install_tool_dependencies,
                                     shed_tool_conf=shed_tool_conf )
             installed_tool_shed_repositories = self.install_repository_revision( trans, **current_payload )

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

@@ -677,6 +677,13 @@ def install_tool_dependencies_with_update( self, trans, **kwd ):
             install_tool_dependencies_check_box_checked = True
         install_tool_dependencies_check_box = CheckboxField( 'install_tool_dependencies',
                                                              checked=install_tool_dependencies_check_box_checked )
+        view = views.DependencyResolversView(self.app)
+        if view.installable_resolvers:
+            install_resolver_dependencies_check_box_checked = True
+        else:
+            install_resolver_dependencies_check_box_checked = False
+        install_resolver_dependencies_check_box = CheckboxField( 'install_resolver_dependencies',
+                                                                 checked=install_resolver_dependencies_check_box_checked )
         return trans.fill_template( '/admin/tool_shed_repository/install_tool_dependencies_with_update.mako',
                                     repository=repository,
                                     updating_repository_id=updating_repository_id,
@@ -686,6 +693,7 @@ def install_tool_dependencies_with_update( self, trans, **kwd ):
                                     encoded_relative_install_dir=encoded_relative_install_dir,
                                     encoded_tool_dependencies_dict=encoded_tool_dependencies_dict,
                                     install_tool_dependencies_check_box=install_tool_dependencies_check_box,
+                                    install_resolver_dependencies_check_box=install_resolver_dependencies_check_box,
                                     tool_dependencies_dict=tool_dependencies_dict,
                                     message=message,
                                     status=status )
@@ -731,8 +739,10 @@ def manage_repositories( self, trans, **kwd ):
                 encoded_kwd = kwd[ 'encoded_kwd' ]
                 decoded_kwd = encoding_util.tool_shed_decode( encoded_kwd )
                 install_tool_dependencies = CheckboxField.is_checked( decoded_kwd.get( 'install_tool_dependencies', '' ) )
+                install_resolver_dependencies = CheckboxField.is_checked( decoded_kwd.get( 'install_resolver_dependencies', '' ) )
                 tsr_ids = decoded_kwd[ 'tool_shed_repository_ids' ]
                 decoded_kwd['install_tool_dependencies'] = install_tool_dependencies
+                decoded_kwd['install_resolver_dependencies'] = install_resolver_dependencies
                 try:
                     tool_shed_repositories = irm.install_repositories(
                         tsr_ids=tsr_ids,
@@ -1223,6 +1233,13 @@ def prepare_for_install( self, trans, **kwd ):
                                                              checked=install_tool_dependencies_check_box_checked )
         # Handle repository dependencies check box.
         install_repository_dependencies_check_box = CheckboxField( 'install_repository_dependencies', checked=True )
+        view = views.DependencyResolversView(self.app)
+        if view.installable_resolvers:
+            install_resolver_dependencies_check_box_checked = True
+        else:
+            install_resolver_dependencies_check_box_checked = False
+        install_resolver_dependencies_check_box = CheckboxField( 'install_resolver_dependencies',
+                                                                 checked=install_resolver_dependencies_check_box_checked )
         encoded_repo_info_dicts = encoding_util.encoding_sep.join( encoded_repo_info_dicts )
         tool_shed_url = kwd[ 'tool_shed_url' ]
         if includes_tools_for_display_in_tool_panel:
@@ -1237,6 +1254,7 @@ def prepare_for_install( self, trans, **kwd ):
                                         includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel,
                                         includes_tool_dependencies=includes_tool_dependencies,
                                         install_tool_dependencies_check_box=install_tool_dependencies_check_box,
+                                        install_resolver_dependencies_check_box=install_resolver_dependencies_check_box,
                                         has_repository_dependencies=has_repository_dependencies,
                                         install_repository_dependencies_check_box=install_repository_dependencies_check_box,
                                         new_tool_panel_section_label=new_tool_panel_section_label,
@@ -1338,6 +1356,7 @@ def reinstall_repository( self, trans, **kwd ):
         no_changes_checked = CheckboxField.is_checked( no_changes )
         install_repository_dependencies = CheckboxField.is_checked( kwd.get( 'install_repository_dependencies', '' ) )
         install_tool_dependencies = CheckboxField.is_checked( kwd.get( 'install_tool_dependencies', '' ) )
+        install_resolver_dependencies = CheckboxField.is_checked( kwd.get( 'install_resolver_dependencies', '' ) )
         shed_tool_conf, tool_path, relative_install_dir = \
             suc.get_tool_panel_config_tool_path_install_dir( trans.app, tool_shed_repository )
         repository_clone_url = common_util.generate_clone_url_for_installed_repository( trans.app, tool_shed_repository )
@@ -1442,6 +1461,7 @@ def reinstall_repository( self, trans, **kwd ):
                         includes_tools=tool_shed_repository.includes_tools,
                         includes_tools_for_display_in_tool_panel=tool_shed_repository.includes_tools_for_display_in_tool_panel,
                         install_tool_dependencies=install_tool_dependencies,
+                        install_resolver_dependencies=install_resolver_dependencies,
                         repo_info_dicts=filtered_repo_info_dicts,
                         message=message,
                         new_tool_panel_section_label=new_tool_panel_section_label,
@@ -1695,6 +1715,13 @@ def reselect_tool_panel_section( self, trans, **kwd ):
         else:
             install_tool_dependencies_check_box_checked = True
         install_tool_dependencies_check_box = CheckboxField( 'install_tool_dependencies', checked=install_tool_dependencies_check_box_checked )
+        view = views.DependencyResolversView(self.app)
+        if view.installable_resolvers:
+            install_resolver_dependencies_check_box_checked = True
+        else:
+            install_resolver_dependencies_check_box_checked = False
+        install_resolver_dependencies_check_box = CheckboxField( 'install_resolver_dependencies',
+                                                                 checked=install_resolver_dependencies_check_box_checked )
         return trans.fill_template( '/admin/tool_shed_repository/reselect_tool_panel_section.mako',
                                     repository=tool_shed_repository,
                                     no_changes_check_box=no_changes_check_box,
@@ -1708,6 +1735,7 @@ def reselect_tool_panel_section( self, trans, **kwd ):
                                     has_repository_dependencies=has_repository_dependencies,
                                     install_repository_dependencies_check_box=install_repository_dependencies_check_box,
                                     install_tool_dependencies_check_box=install_tool_dependencies_check_box,
+                                    install_resolver_dependencies_check_box=install_resolver_dependencies_check_box,
                                     containers_dict=containers_dict,
                                     tool_panel_section_select_field=tool_panel_section_select_field,
                                     shed_tool_conf_select_field=shed_tool_conf_select_field,

lib/tool_shed/galaxy_install/install_manager.py

@@ -725,6 +725,7 @@ def __initiate_and_install_repositories( self, tool_shed_url, repository_revisio
             raise exceptions.InternalServerError( "Tool shed response missing required parameter 'includes_tools_for_display_in_tool_panel'." )
         # Get the information about the Galaxy components (e.g., tool pane section, tool config file, etc) that will contain the repository information.
         install_repository_dependencies = install_options.get( 'install_repository_dependencies', False )
+        install_resolver_dependencies = install_options.get( 'install_resolver_dependencies', False)
         install_tool_dependencies = install_options.get( 'install_tool_dependencies', False )
         if install_tool_dependencies:
             self.__assert_can_install_dependencies()
@@ -766,6 +767,7 @@ def __initiate_and_install_repositories( self, tool_shed_url, repository_revisio
                                       includes_tools=includes_tools,
                                       includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel,
                                       install_repository_dependencies=install_repository_dependencies,
+                                      install_resolver_dependencies=install_resolver_dependencies,
                                       install_tool_dependencies=install_tool_dependencies,
                                       message='',
                                       new_tool_panel_section_label=new_tool_panel_section_label,
@@ -795,6 +797,7 @@ def __initiate_and_install_repositories( self, tool_shed_url, repository_revisio
                 tool_path=tool_path,
                 tool_panel_section_keys=tool_panel_section_keys,
                 repo_info_dicts=filtered_repo_info_dicts,
+                install_resolver_dependencies=install_resolver_dependencies,
                 install_tool_dependencies=install_tool_dependencies,
                 tool_panel_section_mapping=tool_panel_section_mapping,
             )
@@ -806,6 +809,7 @@ def install_repositories( self, tsr_ids, decoded_kwd, reinstalling ):
         tool_panel_section_keys = util.listify( decoded_kwd[ 'tool_panel_section_keys' ] )
         tool_panel_section_mapping = decoded_kwd.get( 'tool_panel_section_mapping', {} )
         repo_info_dicts = util.listify( decoded_kwd[ 'repo_info_dicts' ] )
+        install_resolver_dependencies = decoded_kwd['install_resolver_dependencies']
         install_tool_dependencies = decoded_kwd['install_tool_dependencies']
         filtered_repo_info_dicts = []
         filtered_tool_panel_section_keys = []
@@ -841,6 +845,7 @@ def install_repositories( self, tsr_ids, decoded_kwd, reinstalling ):
                                                    tool_panel_section_key=tool_panel_section_key,
                                                    shed_tool_conf=shed_tool_conf,
                                                    tool_path=tool_path,
+                                                   install_resolver_dependencies=install_resolver_dependencies,
                                                    install_tool_dependencies=install_tool_dependencies,
                                                    reinstalling=reinstalling,
                                                    tool_panel_section_mapping=tool_panel_section_mapping )
@@ -850,7 +855,7 @@ def install_repositories( self, tsr_ids, decoded_kwd, reinstalling ):
         return installed_tool_shed_repositories
 
     def install_tool_shed_repository( self, tool_shed_repository, repo_info_dict, tool_panel_section_key, shed_tool_conf, tool_path,
-                                      install_tool_dependencies, reinstalling=False, tool_panel_section_mapping={} ):
+                                      install_resolver_dependencies, install_tool_dependencies, reinstalling=False, tool_panel_section_mapping={} ):
         self.app.install_model.context.flush()
         if tool_panel_section_key:
             _, tool_section = self.app.toolbox.get_section( tool_panel_section_key )
@@ -908,7 +913,7 @@ def install_tool_shed_repository( self, tool_shed_repository, repo_info_dict, to
                     error_message += "Version information for the tools included in the <b>%s</b> repository is missing.  " % tool_shed_repository.name
                     error_message += "Reset all of this repository's metadata in the tool shed, then set the installed tool versions "
                     error_message += "from the installed repository's <b>Repository Actions</b> menu.  "
-                if install_tool_dependencies:
+                if install_resolver_dependencies:
                     requirements = suc.get_unique_requirements_from_repository(tool_shed_repository)
                     [self._view.install_dependency(id=None, **req) for req in requirements]
             if install_tool_dependencies and tool_shed_repository.tool_dependencies and 'tool_dependencies' in metadata:

templates/admin/tool_shed_repository/common.mako

@@ -65,7 +65,7 @@
     </script>
 </%def>
 
-<%def name="render_dependencies_section( repository_dependencies_check_box, install_tool_dependencies_check_box, containers_dict, revision_label=None, export=False )">
+<%def name="render_dependencies_section( repository_dependencies_check_box, install_tool_dependencies_check_box, install_resolver_dependencies_check_box, containers_dict, revision_label=None, export=False )">
     <style type="text/css">
         #dependency_table{ table-layout:fixed;
                            width:100%;
@@ -110,6 +110,14 @@
             </p>
         </div>
     </div>
+    <div class="form-row">
+        <label>Install resolvable dependencies (Currently conda-only) ?</label>
+        ${install_resolver_dependencies_check_box.get_html()}
+        <div class="toolParamHelp" style="clear: both;">
+            Un-check to skip automatic installation of tool dependencies.
+        </div>
+    </div>
+    <div style="clear: both"></div>
     %if repository_dependencies_root_folder or missing_repository_dependencies_root_folder:
         %if repository_dependencies_check_box is not None:
             <div class="form-row">

templates/admin/tool_shed_repository/preview_repository.mako

@@ -307,6 +307,7 @@ function changeset_metadata() {
         }
         $("#tool_dependencies").show();
         $("#install_tool_dependencies").prop('disabled', false);
+        $("#install_resolver_dependencies_checkbox").show();
         $("#install_tool_dependencies_checkbox").show();
     }
     else {
@@ -359,6 +360,7 @@ $(function() {
         form.preventDefault();
         var params = {};
         params.tool_shed_url = $("#tool_shed_url").val();
+        params.install_resolver_dependencies = $("#install_resolver_dependencies").val();
         params.install_tool_dependencies = $("#install_tool_dependencies").val();
         params.install_repository_dependencies = $("#install_repository_dependencies").val();
         params.tool_panel_section = JSON.stringify(select_tps(params));
@@ -423,6 +425,10 @@ $(function() {
         </div>
         <div class="toolFormTitle">Contents of this repository at revision <strong id="current_changeset"></strong></div>
         <div class="toolFormBody">
+            <p id="install_resolver_dependencies_checkbox">
+                <input type="checkbox" checked id="install_resolver_dependencies" />
+                <label for="install_resolver_dependencies">Install resolver dependencies</label>
+            </p>
             <p id="install_repository_dependencies_checkbox">
                 <input type="checkbox" checked id="install_repository_dependencies" />
                 <label for="install_repository_dependencies">Install repository dependencies</label>

templates/admin/tool_shed_repository/reselect_tool_panel_section.mako

@@ -42,7 +42,7 @@
                         <th bgcolor="#EBD9B2">Confirm dependency installation</th>
                     </table>
                 </div>
-                ${render_dependencies_section( install_repository_dependencies_check_box, install_tool_dependencies_check_box, containers_dict, revision_label=None, export=False )}
+                ${render_dependencies_section( install_resolver_dependencies_check_box, install_repository_dependencies_check_box, install_tool_dependencies_check_box, containers_dict, revision_label=None, export=False )}
             %endif
             %if shed_tool_conf_select_field:
                 <div class="form-row">

templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako

@@ -90,7 +90,7 @@
                         <th bgcolor="#EBD9B2">Confirm dependency installation</th>
                     </table>
                 </div>
-                ${render_dependencies_section( install_repository_dependencies_check_box, install_tool_dependencies_check_box, containers_dict, revision_label=None, export=False )}
+                ${render_dependencies_section( install_resolver_dependencies_check_box, install_repository_dependencies_check_box, install_tool_dependencies_check_box, containers_dict, revision_label=None, export=False )}
                 <div style="clear: both"></div>
             %endif
             <div class="form-row">

templates/admin/tool_shed_repository/select_tool_panel_section.mako

@@ -90,7 +90,7 @@
                         <th bgcolor="#EBD9B2">Confirm dependency installation</th>
                     </table>
                 </div>
-                ${render_dependencies_section( install_repository_dependencies_check_box, install_tool_dependencies_check_box, containers_dict, revision_label=None, export=False )}
+                ${render_dependencies_section( install_resolver_dependencies_check_box, install_repository_dependencies_check_box, install_tool_dependencies_check_box, containers_dict, revision_label=None, export=False )}
                 <div style="clear: both"></div>
             %endif
             %if shed_tool_conf_select_field: