Merge branch 'v0.8.4' into encyclopedia-api

nomad/metainfo/legacy.py

@@ -22,6 +22,7 @@ from typing import cast, Dict, List, Union, Any, Set, Iterable, Tuple
 import numpy as np
 from pint.errors import UndefinedUnitError
 import os.path
+import importlib
 
 
 from nomadcore.local_meta_info import loadJsonFile, InfoKindEl, InfoKindEnv
@@ -105,6 +106,22 @@ class LegacyMetainfoEnvironment(Environment):
     the environment.
     '''
 
+    @staticmethod
+    def from_legacy_package_path(path):
+        metainfo_package_name = os.path.basename(path)
+        package = metainfo_package_name
+        if package.endswith('.nomadmetainfo.json'):
+            package = package[:-19]
+        if package.endswith('.json'):
+            package = package[:-5]
+
+        python_package_name, _ = python_package_mapping(package)
+        python_package_name = '.'.join(python_package_name.split('.')[:-1])
+        python_module = importlib.import_module(python_package_name)
+        metainfo = getattr(python_module, 'm_env')
+
+        return metainfo
+
     legacy_package_name = Quantity(type=str)
 
     def __init__(self, *args, **kwargs):

nomad/metainfo/metainfo.py

@@ -31,7 +31,7 @@ import pytz
 import docstring_parser
 import jmespath
 
-from nomad.units import ureg
+from nomad.units import ureg as units
 
 
 m_package: 'Package' = None
@@ -133,7 +133,7 @@ class SectionProxy(MProxy):
     def m_proxy_resolve(self):
         if self.m_proxy_section and not self.m_proxy_resolved:
             root = self.m_proxy_section
-            while root is not None and not isinstance(root, Package):
+            while root.m_parent is not None and not isinstance(root, Package):
                 root = root.m_parent
 
             if isinstance(root, Package):
@@ -221,7 +221,7 @@ class _Dimension(DataType):
 class _Unit(DataType):
     def set_normalize(self, section, quantity_def: 'Quantity', value):
         if isinstance(value, str):
-            value = ureg.parse_units(value)
+            value = units.parse_units(value)
 
         elif not isinstance(value, pint.unit._Unit):
             raise TypeError('Units must be given as str or pint Unit instances.')
@@ -232,7 +232,7 @@ class _Unit(DataType):
         return value.__str__()
 
     def deserialize(self, section, quantity_def: 'Quantity', value):
-        return ureg.parse_units(value)
+        return units.parse_units(value)
 
 
 class _Callable(DataType):
@@ -344,7 +344,7 @@ class Reference(DataType):
     def set_normalize(self, section: 'MSection', quantity_def: 'Quantity', value: Any) -> Any:
         if isinstance(self.target_section_def, MProxy):
             proxy = self.target_section_def
-            proxy.m_proxy_section = section
+            proxy.m_proxy_section = section.m_def
             proxy.m_proxy_quantity = quantity_def
             self.target_section_def = proxy.m_proxy_resolve()
 

nomad/normalizing/normalizer.py

@@ -34,6 +34,7 @@ class Normalizer(metaclass=ABCMeta):
 
     def __init__(self, backend: Backend) -> None:
         self._backend = backend
+        self.entry_archive = backend.entry_archive
         try:
             self.section_run = backend.entry_archive.section_run[0]
         except (AttributeError, IndexError):

nomad/processing/data.py

@@ -1076,7 +1076,7 @@ class Upload(Proc):
             '',
             'your data %suploaded at %s has completed processing.' % (
                 '"%s" ' % self.name if self.name else '', self.upload_time.isoformat()),  # pylint: disable=no-member
-            'You can review your data on your upload page: %s' % config.gui_url(),
+            'You can review your data on your upload page: %s' % config.gui_url(page='uploads'),
             '',
             'If you encounter any issues with your upload, please let us know and reply to this email.',
             '',

nomad/search.py

@@ -23,7 +23,7 @@ from elasticsearch.exceptions import NotFoundError
 from datetime import datetime
 import json
 
-from nomad import config, datamodel, infrastructure, datamodel, utils
+from nomad import config, datamodel, infrastructure, utils
 from nomad.metainfo.search_extension import search_quantities, metrics, order_default_quantities
 
 

ops/helm/nomad/templates/nomad-configmap.yml

@@ -11,6 +11,10 @@ data:
   nomad.yaml: |
     meta:
       release: "{{ .Release.Name }}"
+      service: "{{ .Values.meta.service }}"
+      homepage: "{{ .Values.meta.homepage }}"
+      source_url: "{{ .Values.meta.source_url }}"
+      maintainer_email: "{{ .Values.meta.maintainer_email }}"
     reprocess_unmatched: {{ .Values.reprocess_unmatched }}
     fs:
       tmp: "{{ .Values.volumes.tmp }}"

ops/helm/nomad/values.yaml

@@ -5,6 +5,12 @@ version:
   usesBetaData: false
   officialUrl: "https://nomad-lab.eu/prod/rae/gui"
 
+meta:
+  service: "app"
+  homepage: "https://nomad-lab.eu"
+  source_url: "https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR"
+  maintainer_email: "markus.scheidgen@physik.hu-berlin.de"
+
 ## Everything concerning the container images to be used
 image:
   ## The kubernetes docker-registry secret that can be used to access the registry

tests/metainfo/test_metainfo.py

@@ -20,7 +20,7 @@ import datetime
 from nomad.metainfo.metainfo import (
     MSection, MCategory, Section, Quantity, SubSection, Definition, Package, DeriveError,
     MetainfoError, Environment, MResource, Datetime, Annotation, SectionAnnotation,
-    DefinitionAnnotation, Reference, MProxy, derived)
+    DefinitionAnnotation, Reference, MProxy, derived, SectionProxy)
 from nomad.metainfo.example import Run, VaspRun, System, SystemHash, Parsing, SCC, m_package as example_package
 from nomad import utils
 from nomad.units import ureg
@@ -585,6 +585,24 @@ class TestM1:
         obj = ReferencingSection.m_from_dict(obj.m_to_dict(with_meta=True))
         assert obj.proxy.name == 'test_value'
 
+    def test_ref_with_section_proxy(self):
+        package = Package(name='test_package')
+
+        class OtherSection(MSection):
+            name = Quantity(type=str)
+
+        class ReferencingSection(MSection):
+            reference = Quantity(type=Reference(SectionProxy('OtherSection')))
+
+        package.m_add_sub_section(Package.section_definitions, OtherSection.m_def)
+        package.m_add_sub_section(Package.section_definitions, ReferencingSection.m_def)
+
+        referencing = ReferencingSection()
+        reference = OtherSection()
+        referencing.reference = reference
+
+        assert referencing.reference == reference
+
     def test_copy(self):
         run = Run()
         run.m_create(Parsing).parser_name = 'test'