Fixed resoursive adding of sections to resources.

nomad/metainfo/metainfo.py

@@ -521,8 +521,23 @@ class MResource():
         return cast(MSectionBound, result)
 
     def add(self, section):
-        section.m_resource = self
-        self.__data.setdefault(section.m_def, []).append(section)
+        '''
+        Add the given section to this resource. Will also add all its contents to the
+        resource and make all contest available for :func:`all`. Will also remove
+        all contents from possible other resources. A section can only be contained in
+        one resource at a time.
+
+        This is potentially expensive. Do not add a section that already has a deep tree
+        of sub-sections. Ideally, add the root section first. If you create sub sections
+        afterwards, they will be automatically added to this resource.
+        '''
+        if section.m_resource is not None:
+            section.m_resource.remove(section)
+
+        for content in section.m_all_contents(include_self=True):
+            content.m_resource = self
+            self.__data.setdefault(content.m_def, []).append(content)
+
         if section.m_parent is None:
             self.contents.append(section)
 

nomad/processing/data.py

@@ -414,7 +414,7 @@ class Calc(Proc):
         information in section_encyclopedia as well as the DFT domain metadata.
         """
         try:
-            logger = self.get_logger(**context)
+            logger = self.get_logger(parser=self.parser, step=self.parser)
 
             # Open the archive of the phonon calculation.
             upload_files = StagingUploadFiles(self.upload_id, is_authorized=lambda: True)
@@ -425,7 +425,6 @@ class Calc(Proc):
             self._calc_proc_logs = phonon_archive.processing_logs
 
             # Re-create a backend
-            context = dict(parser=self.parser, step=self.parser)
             metainfo = phonopyparser.metainfo.m_env
             self._parser_backend = Backend(metainfo, logger=logger, domain="dft")
             self._parser_backend.entry_archive = phonon_archive

tests/metainfo/test_metainfo.py

@@ -519,6 +519,22 @@ class TestM1:
 
         assert len(resource.all(System)) == 2
 
+    def test_resource_add(self):
+        # adding
+        resource = MResource()
+        run = Run()
+        resource.add(run)
+        run.m_create(System)
+        run.m_create(System)
+        assert len(resource.all(Run)) == 1
+        assert len(resource.all(System)) == 2
+
+        # implicitly moving to another resource
+        resource = MResource()
+        resource.add(run)
+        assert len(resource.all(Run)) == 1
+        assert len(resource.all(System)) == 2
+
     def test_resource_move(self):
         resource = MResource()
         run = resource.create(Run)