Use resolver to explicitly install dependencies

This avoids replicating the resolver logic when installing dependencies
and should be better than https://github.com/jmchilton/galaxy/pull/52

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

@@ -145,7 +145,7 @@ class CondaDependencyResolver(DependencyResolver, ListableDependencyResolver, In
         dependencies = []
 
         is_installed = self.conda_context.has_env(env)
-        if not is_installed and self.auto_install:
+        if not is_installed and (self.auto_install or kwds.get('install', False)):
             is_installed = self.install_all(conda_targets)
 
         if is_installed:
@@ -191,7 +191,7 @@ class CondaDependencyResolver(DependencyResolver, ListableDependencyResolver, In
         preserve_python_environment = kwds.get("preserve_python_environment", False)
 
         job_directory = kwds.get("job_directory", None)
-        if not is_installed and self.auto_install and job_directory:
+        if not is_installed and (self.auto_install or kwds.get('install', False)):
             is_installed = self.install_dependency(name=name, version=version, type=type)
 
         if not is_installed:

lib/galaxy/tools/deps/views.py

@@ -45,6 +45,9 @@ class DependencyResolversView(object):
     def resolver_dependency(self, index, **kwds):
         return self._dependency(**kwds)
 
+    def install_dependencies(self, requirements):
+        return self._dependency_manager._requirements_to_dependencies_dict(requirements, **{'install': True})
+
     def install_dependency(self, index=None, **payload):
         """
         Installs dependency using highest priority resolver that supports dependency installation

lib/galaxy/webapps/galaxy/api/tools.py

@@ -141,11 +141,11 @@ class ToolsController( BaseAPIController, UsesVisualizationMixin ):
             force_rebuild:           If true and chache dir exists, attempts to delete cache dir
         """
         tool = self._get_tool(id)
-        [tool._view.install_dependency(id=None, **req.to_dict()) for req in tool.requirements]
+        tool._view.install_dependencies(tool.requirements)
         if kwds.get('build_dependency_cache'):
             tool.build_dependency_cache(**kwds)
         # TODO: rework resolver install system to log and report what has been done.
-        # _view.install_dependency should return a dict with stdout, stderr and success status
+        # _view.install_dependencies should return a dict with stdout, stderr and success status
         return tool.tool_requirements_status
 
     @expose_api

lib/tool_shed/galaxy_install/install_manager.py

@@ -905,15 +905,15 @@ class InstallRepositoryManager( object ):
             if 'tools' in metadata and install_resolver_dependencies:
                 self.update_tool_shed_repository_status( tool_shed_repository,
                                                          self.install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES )
-                requirements = suc.get_unique_requirements_from_repository(tool_shed_repository)
-                [self._view.install_dependency(id=None, **req) for req in requirements]
-                if self.app.config.use_cached_dependency_manager:
-                    cached_requirements = []
-                    for tool_d in metadata['tools']:
-                        tool = self.app.toolbox._tools_by_id.get(tool_d['guid'], None)
-                        if tool and tool.requirements not in cached_requirements:
-                            cached_requirements.append(tool.requirements)
+                installed_requirements = []
+                for tool_d in metadata['tools']:
+                    tool = self.app.toolbox._tools_by_id.get(tool_d['guid'], None)
+                    if tool and tool.requirements not in installed_requirements:
+                        self._view.install_dependencies(tool.requirements)
+                        installed_requirements.append(tool.requirements)
+                        if self.app.config.use_cached_dependency_manager:
                             tool.build_dependency_cache()
+
             if install_tool_dependencies and tool_shed_repository.tool_dependencies and 'tool_dependencies' in metadata:
                 work_dir = tempfile.mkdtemp( prefix="tmp-toolshed-itsr" )
                 # Install tool dependencies.