Revert mako hack to always display install_tool_dependency button

- Add resolver checkbox
 - Add possibility to disable resolvers if initialization failed

lib/galaxy/tools/deps/resolvers/__init__.py

@@ -13,6 +13,7 @@ class DependencyResolver(Dictifiable, object):
     # because the repository install context is used in dependency resolution
     # so the same requirement tags in different tools will have very different
     # resolution.
+    disabled = False
     resolves_simple_dependencies = True
     __metaclass__ = ABCMeta
 

lib/galaxy/tools/deps/resolvers/conda.py

@@ -89,9 +89,14 @@ class CondaDependencyResolver(DependencyResolver, ListableDependencyResolver, In
         auto_install = _string_as_bool(get_option("auto_install"))
         copy_dependencies = _string_as_bool(get_option("copy_dependencies"))
 
-        if auto_init and not os.path.exists(conda_context.conda_prefix):
-            if install_conda(conda_context):
-                raise Exception("Conda installation requested and failed.")
+        if not os.path.exists(conda_context.conda_prefix):
+            if auto_init:
+                if install_conda(conda_context):
+                    self.disabled = True
+                    log.warning("Conda installation requested and failed.")
+            else:
+                self.disabled = True
+                log.warning("Conda not installed and auto-installation disabled.")
 
         self.conda_context = conda_context
         self.auto_install = auto_install

lib/galaxy/tools/deps/views.py

@@ -121,9 +121,9 @@ class DependencyResolversView(object):
     @property
     def installable_resolvers(self):
         """
-        List index for all resolvers that have the 'install_dependency' attribute
+        List index for all active resolvers that have the 'install_dependency' attribute
         """
-        return [index for index, resolver in enumerate(self._dependency_resolvers) if hasattr(resolver, "install_dependency")]
+        return [index for index, resolver in enumerate(self._dependency_resolvers) if hasattr(resolver, "install_dependency") and not resolver.disabled ]
 
     def get_requirements_status(self, requested_requirements):
         result = []

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

@@ -692,8 +692,8 @@ class AdminToolshed( AdminGalaxy ):
                                     encoded_updated_metadata=encoded_updated_metadata,
                                     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,
+                                    install_tool_dependencies_check_box=install_tool_dependencies_check_box,
                                     tool_dependencies_dict=tool_dependencies_dict,
                                     message=message,
                                     status=status )
@@ -738,11 +738,11 @@ class AdminToolshed( AdminGalaxy ):
                 reinstalling = util.string_as_bool( kwd.get( 'reinstalling', False ) )
                 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', '' ) )
+                install_tool_dependencies = CheckboxField.is_checked( decoded_kwd.get( 'install_tool_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
+                decoded_kwd['install_tool_dependencies'] = install_tool_dependencies
                 try:
                     tool_shed_repositories = irm.install_repositories(
                         tsr_ids=tsr_ids,
@@ -1099,7 +1099,7 @@ class AdminToolshed( AdminGalaxy ):
                 install_tool_dependencies = CheckboxField.is_checked( install_tool_dependencies )
             else:
                 install_tool_dependencies = False
-            install_repository_dependencies = CheckboxField.is_checked( install_resolver_dependencies )
+            install_resolver_dependencies = CheckboxField.is_checked( install_resolver_dependencies )
             tool_path = suc.get_tool_path_by_shed_tool_conf_filename( trans.app, shed_tool_conf )
             installation_dict = dict( install_repository_dependencies=install_repository_dependencies,
                                       new_tool_panel_section_label=new_tool_panel_section_label,
@@ -1283,6 +1283,7 @@ class AdminToolshed( AdminGalaxy ):
                                         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,

lib/tool_shed/galaxy_install/repair_repository_manager.py

@@ -194,6 +194,7 @@ class RepairRepositoryManager():
                                               shed_tool_conf,
                                               tool_path,
                                               install_tool_dependencies=True,
+                                              install_resolver_dependencies=False,  # Assuming repairs are only necessary toolshed packages
                                               reinstalling=True )
             if repository.status in [ self.app.install_model.ToolShedRepository.installation_status.ERROR ]:
                 repair_dict = add_repair_dict_entry( repository.name, repository.error_message )

templates/admin/tool_shed_repository/common.mako

@@ -110,6 +110,7 @@
             </p>
         </div>
     </div>
+    %if install_resolver_dependencies_check_box:
     <div class="form-row">
         <label>Install resolvable dependencies (Currently conda-only) ?</label>
         ${install_resolver_dependencies_check_box.get_html()}
@@ -117,9 +118,10 @@
             Un-check to skip automatic installation of tool dependencies.
         </div>
     </div>
+    %endif
     <div style="clear: both"></div>
     %if repository_dependencies_root_folder or missing_repository_dependencies_root_folder:
-        %if repository_dependencies_check_box is not None:
+        %if repository_dependencies_check_box:
             <div class="form-row">
                 %if export:
                     <label>Export repository dependencies?</label>
@@ -159,19 +161,20 @@
         %endif
     %endif
     %if tool_dependencies_root_folder or missing_tool_dependencies_root_folder:
-        <div class="form-row">
-            <label>Handle tool dependencies?</label>
-            <% disabled = trans.app.config.tool_dependency_dir is None %>
-            ${install_tool_dependencies_check_box.get_html( disabled=disabled )}
-            <div class="toolParamHelp" style="clear: both;">
-                %if disabled:
-                    Set the tool_dependency_dir configuration value in your Galaxy config to automatically handle tool dependencies.
-                %else:
-                    Un-check to skip automatic handling of tool dependencies (if any).
-                %endif
-            </div>
-        </div>
-        <div style="clear: both"></div>
+        %if install_tool_dependencies_check_box is not None:
+            <div class="form-row">
+                <label>Handle tool dependencies?</label>
+                <% disabled = trans.app.config.tool_dependency_dir is None %>
+                ${install_tool_dependencies_check_box.get_html( disabled=disabled )}
+                <div class="toolParamHelp" style="clear: both;">
+                    %if disabled:
+                        Set the tool_dependency_dir configuration value in your Galaxy config to automatically handle tool dependencies.
+                    %else:
+                        Un-check to skip automatic handling of these tool dependencies.
+                    %endif
+                </div>
+            <div style="clear: both"></div>
+        %endif
         %if tool_dependencies_root_folder:
             <div class="form-row">
                 <p/>

templates/webapps/tool_shed/repository/export_repository.mako

@@ -34,7 +34,7 @@ ${render_tool_shed_repository_actions( repository, metadata=metadata, changeset_
     <div class="toolFormBody">
         <form name="export_repository" id="export_repository" action="${h.url_for( controller='repository', action='export', repository_id=trans.security.encode_id( repository.id ), changeset_revision=changeset_revision )}" method="post" >
             %if containers_dict is not None and export_repository_dependencies_check_box is not None:
-                ${render_dependencies_section( export_repository_dependencies_check_box, None, containers_dict, revision_label=revision_label, export=True )}
+                ${render_dependencies_section( None, export_repository_dependencies_check_box, None, containers_dict, revision_label=revision_label, export=True )}
                 <div style="clear: both"></div>
             %else:
                 No repository dependencies are defined for revision <b>${revision_label}</b> of this repository, so click <b>Export</b> to export the selected revision.

test/shed_functional/base/twilltestcase.py

@@ -947,7 +947,7 @@ class ShedTwillTestCase( TwillTestCase ):
         repository_ids = self.initiate_installation_process()
         self.wait_for_repository_installation( repository_ids )
 
-    def install_repository( self, name, owner, category_name, install_tool_dependencies=False,
+    def install_repository( self, name, owner, category_name, install_resolver_dependencies=False, install_tool_dependencies=False,
                             install_repository_dependencies=True, changeset_revision=None,
                             strings_displayed=None, strings_not_displayed=None, preview_strings_displayed=None,
                             post_submit_strings_displayed=None, new_tool_panel_section_label=None, includes_tools_for_display_in_tool_panel=True,
@@ -971,6 +971,7 @@ class ShedTwillTestCase( TwillTestCase ):
         assert form is not None, 'Could not find form select_shed_tool_panel_config or select_tool_panel_section.'
         kwd = self.set_form_value( form, kwd, 'install_tool_dependencies', install_tool_dependencies )
         kwd = self.set_form_value( form, kwd, 'install_repository_dependencies', install_repository_dependencies )
+        kwd = self.set_form_value( form, kwd, 'install_resolver_dependencies', install_resolver_dependencies )
         kwd = self.set_form_value( form, kwd, 'shed_tool_conf', self.shed_tool_conf )
         if new_tool_panel_section_label is not None:
             kwd = self.set_form_value( form, kwd, 'new_tool_panel_section_label', new_tool_panel_section_label )