Merge branch 'release_17.05' into release_17.09

lib/galaxy/jobs/__init__.py

@@ -884,6 +884,9 @@ class JobWrapper(object, HasResourceParameters):
         self.galaxy_lib_dir
         # Shell fragment to inject dependencies
         self.dependency_shell_commands = self.tool.build_dependency_shell_commands(job_directory=self.working_directory)
+        if self.tool.requires_galaxy_python_environment:
+            # These tools (upload, metadata, data_source) may need access to the datatypes registry.
+            self.app.datatypes_registry.to_xml_file(os.path.join(self.working_directory, 'registry.xml'))
         # We need command_line persisted to the db in order for Galaxy to re-queue the job
         # if the server was stopped and restarted before the job finished
         job.command_line = unicodify(self.command_line)

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

@@ -173,6 +173,14 @@ class ModuleDependency(Dependency):
         self.module_version = module_version
         self._exact = exact
 
+    @property
+    def name(self):
+        return self.module_name
+
+    @property
+    def version(self):
+        return self.module_version
+
     @property
     def exact(self):
         return self._exact

test/unit/jobs/test_job_wrapper.py

@@ -162,6 +162,7 @@ class MockTool(object):
         self.version_string_cmd = TEST_VERSION_COMMAND
         self.tool_dir = "/path/to/tools"
         self.dependencies = []
+        self.requires_galaxy_python_environment = False
 
     def build_dependency_shell_commands(self, job_directory):
         return TEST_DEPENDENCIES_COMMANDS