Revert "Create merged environments at install time"

This reverts commit 0e509a98ed.

lib/galaxy/tools/deps/__init__.py

@@ -118,19 +118,6 @@ class DependencyManager( object ):
 
         return requirement_to_dependency
 
-    def install_all(self, requirements):
-        """
-        Attempt to install all requirements at once.
-        If sucessfull returns True, else returns False
-        """
-        for resolver in self.dependency_resolvers:
-            if hasattr(resolver, 'get_targets') and hasattr(resolver, 'install_all'):
-                targets = resolver.get_targets(requirements)
-                is_installed = resolver.install_all(targets)
-                if is_installed:
-                    return True
-        return False
-
     def _requirements_to_dependencies_dict(self, requirements, **kwds):
         """Build simple requirements to dependencies dict for resolution."""
         requirement_to_dependency = OrderedDict()

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

@@ -120,7 +120,7 @@ class CondaDependencyResolver(DependencyResolver, ListableDependencyResolver, In
 
         return is_installed
 
-    def _get_conda_targets(self, requirements):
+    def resolve_all(self, requirements, **kwds):
         if len(requirements) == 0:
             return False
 
@@ -138,15 +138,6 @@ class CondaDependencyResolver(DependencyResolver, ListableDependencyResolver, In
                 version = None
 
             conda_targets.append(CondaTarget(requirement.name, version=version))
-        return conda_targets
-
-    def get_targets(self, requirements):
-        return self._get_conda_targets(requirements)
-
-    def resolve_all(self, requirements, **kwds):
-        conda_targets = self.get_targets(requirements)
-        if not conda_targets:
-            return False
 
         preserve_python_environment = kwds.get("preserve_python_environment", False)
 

lib/galaxy/tools/deps/views.py

@@ -45,11 +45,6 @@ class DependencyResolversView(object):
     def resolver_dependency(self, index, **kwds):
         return self._dependency(**kwds)
 
-    def install_dependencies(self, index, requirements):
-        is_installed = self._dependency_manager.install_all(requirements)
-        if not is_installed:
-            return [self.install_dependency(index, req) for req in requirements]
-
     def install_dependency(self, index=None, **payload):
         """
         Installs dependency using highest priority resolver that supports dependency installation

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

@@ -141,9 +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_dependencies(None, tool.requirements)
+        [tool._view.install_dependency(id=None, **req.to_dict()) for req in 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_dependencies should return a dict with stdout, stderr and success status
+        # _view.install_dependency 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

@@ -905,12 +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 )
-                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:
-                        installed_requirements.append(tool.requirements)
-                        self._view.install_dependencies(None, tool.requirements)
+                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)
+                            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.