Merge pull request #7939 from mvdbeek/jmchilton-objectstore_fix

Fix non-eager object store with nested object stores

test/base/driver_util.py

@@ -240,6 +240,36 @@ def setup_galaxy_config(
     )
     config.update(database_conf(tmpdir, prefer_template_database=prefer_template_database))
     config.update(install_database_conf(tmpdir, default_merged=default_install_db_merged))
+    if asbool(os.environ.get("GALAXY_TEST_USE_HIERARCHICAL_OBJECT_STORE")):
+        object_store_config = os.path.join(tmpdir, "object_store_conf.yml")
+        with open(object_store_config, "w") as f:
+            contents = """
+type: hierarchical
+backends:
+   - id: files1
+     type: disk
+     weight: 1
+     files_dir: "${temp_directory}/files1"
+     extra_dirs:
+     - type: temp
+       path: "${temp_directory}/tmp1"
+     - type: job_work
+       path: "${temp_directory}/job_working_directory1"
+   - id: files2
+     type: disk
+     weight: 1
+     files_dir: "${temp_directory}/files2"
+     extra_dirs:
+     - type: temp
+       path: "${temp_directory}/tmp2"
+     - type: job_work
+       path: "${temp_directory}/job_working_directory2"
+"""
+            contents_template = string.Template(contents)
+            expanded_contents = contents_template.safe_substitute(temp_directory=tmpdir)
+            f.write(expanded_contents)
+        config["object_store_config_file"] = object_store_config
+
     if datatypes_conf is not None:
         config['datatypes_config_file'] = datatypes_conf
     if enable_tool_shed_check:

test/unit/jobs/test_job_wrapper.py

@@ -191,6 +191,9 @@ class MockObjectStore(object):
     def create(self, *args, **kwds):
         pass
 
+    def exists(self, *args, **kwargs):
+        return True
+
     def get_filename(self, *args, **kwds):
         if kwds.get("base_dir", "") == "job_work":
             return self.working_directory

test/unit/test_model_store.py

@@ -283,6 +283,7 @@ def test_import_export_composite_datasets():
     h = model.History(name="Test History", user=u)
 
     d1 = _create_datasets(sa_session, h, 1, extension="html")[0]
+    d1.dataset.create_extra_files_path()
     sa_session.add_all((h, d1))
     sa_session.flush()
 

test/unit/tools/test_actions.py

@@ -274,6 +274,9 @@ class MockObjectStore(object):
         self.first_create = True
         self.object_store_id = "mycoolid"
 
+    def exists(self, *args, **kwargs):
+        return True
+
     def create(self, dataset):
         self.created_datasets.append(dataset)
         if self.first_create:

test/unit/tools/test_collect_primary_datasets.py

@@ -408,6 +408,9 @@ class MockObjectStore(object):
         path = self.created_datasets[dataset]
         return os.stat(path).st_size
 
+    def exists(self, *args, **kwargs):
+        return True
+
     def get_filename(self, dataset):
         return self.created_datasets[dataset]