diff --git a/nomad/graph/graph_reader.py b/nomad/graph/graph_reader.py
index 84ee4b7f169926fddb6321f01e24312b37421bdb..cdf50b86c418e9fcf42a95180b478da5a1f127c3 100644
--- a/nomad/graph/graph_reader.py
+++ b/nomad/graph/graph_reader.py
@@ -58,6 +58,7 @@ from nomad.archive import ArchiveDict, ArchiveList, to_json
from nomad.archive.storage_v2 import ArchiveDict as ArchiveDictNew
from nomad.archive.storage_v2 import ArchiveList as ArchiveListNew
from nomad.datamodel import Dataset, EntryArchive, ServerContext, User
+from nomad.datamodel.metainfo.plot import PlotlyFigure
from nomad.datamodel.util import parse_path
from nomad.files import RawPathInfo, UploadFiles
from nomad.graph.lazy_wrapper import (
@@ -259,7 +260,7 @@ class GraphNode:
raise ArchiveError(f'Circular reference detected: {reference_url}.')
try:
- target = await self.__goto_path(self.archive_root, path_stack)
+ target = await _goto_path(self.archive_root, path_stack)
except (KeyError, IndexError):
raise ArchiveError(f'Archive {self.entry_id} does not contain {reference}.')
@@ -317,7 +318,7 @@ class GraphNode:
try:
# now go to the target path
- other_target = await self.__goto_path(other_archive_root, path_stack)
+ other_target = await _goto_path(other_archive_root, path_stack)
except (KeyError, IndexError):
raise ArchiveError(f'Archive {other_entry_id} does not contain {path}.')
@@ -352,16 +353,14 @@ class GraphNode:
result_root=self.ref_result_root,
)
- @staticmethod
- async def __goto_path(target_root: ArchiveDict | dict, path_stack: list) -> Any:
- """
- Go to the specified path in the data.
- """
- for key in path_stack:
- target_root = await goto_child(
- target_root, int(key) if key.isdigit() else key
- )
- return target_root
+
+async def _goto_path(target_root: GenericDict, path_stack: list) -> Any:
+ """
+ Go to the specified path in the data.
+ """
+ for key in path_stack:
+ target_root = await goto_child(target_root, int(key) if key.isdigit() else key)
+ return target_root
async def _if_exists(target_root: dict, path_stack: list) -> bool:
@@ -424,7 +423,7 @@ def _convert_ref_to_path_string(ref: str, upload_id: str = None) -> str:
def _to_response_config(config: RequestConfig, exclude: list = None, **kwargs):
- response_config = config.dict(exclude_unset=True, exclude_none=True)
+ response_config = config.model_dump(exclude_unset=True, exclude_none=True)
for item in ('include', 'exclude'):
if isinstance(x := response_config.pop(item, None), frozenset):
@@ -989,7 +988,7 @@ class GeneralReader:
@staticmethod
async def _overwrite_upload(item: Upload):
plain_dict = orjson.loads(
- upload_to_pydantic(item, include_total_count=False).json()
+ upload_to_pydantic(item, include_total_count=False).model_dump_json()
)
plain_dict.pop('entries', None)
cached_item = CachedUpload(item)
@@ -1026,7 +1025,7 @@ class GeneralReader:
@staticmethod
def _overwrite_entry(item: Entry):
- plain_dict = orjson.loads(entry_to_pydantic(item).json())
+ plain_dict = orjson.loads(entry_to_pydantic(item).model_dump_json())
plain_dict.pop('entry_metadata', None)
if mainfile := plain_dict.pop('mainfile', None):
plain_dict['mainfile_path'] = mainfile
@@ -1334,7 +1333,7 @@ class MongoReader(GeneralReader):
if config.query:
assert isinstance(config.query, Metadata)
- search_query = config.query.dict(exclude_none=True) # type: ignore
+ search_query = config.query.model_dump(exclude_none=True) # type: ignore
if config.query.owner:
search_params['owner'] = config.query.owner
@@ -1391,7 +1390,9 @@ class MongoReader(GeneralReader):
references |= Q(references__regex=item)
mongo_query &= references
- return config.query.dict(exclude_unset=True), self.entries.filter(mongo_query)
+ return config.query.model_dump(exclude_unset=True), self.entries.filter(
+ mongo_query
+ )
async def _query_uploads(self, config: RequestConfig):
if not config.query:
@@ -1424,7 +1425,9 @@ class MongoReader(GeneralReader):
elif config.query.is_owned is False:
mongo_query &= Q(main_author__ne=self.auth_user_id)
- return config.query.dict(exclude_unset=True), self.uploads.filter(mongo_query)
+ return config.query.model_dump(exclude_unset=True), self.uploads.filter(
+ mongo_query
+ )
async def _query_datasets(self, config: RequestConfig):
if not config.query:
@@ -1448,7 +1451,9 @@ class MongoReader(GeneralReader):
dataset_name=re.compile(rf'^{config.query.prefix}.*$', re.IGNORECASE)
)
- return config.query.dict(exclude_unset=True), self.datasets.filter(mongo_query)
+ return config.query.model_dump(exclude_unset=True), self.datasets.filter(
+ mongo_query
+ )
@staticmethod
async def _query_groups(config: RequestConfig):
@@ -1457,7 +1462,7 @@ class MongoReader(GeneralReader):
if isinstance(config.query, UserGroupQuery)
else UserGroupQuery()
)
- return query.dict(exclude_unset=True), MongoUserGroup.get_by_query(query)
+ return query.model_dump(exclude_unset=True), MongoUserGroup.get_by_query(query)
async def _normalise(
self, mongo_result, config: RequestConfig, transformer: Callable
@@ -1473,7 +1478,7 @@ class MongoReader(GeneralReader):
elif isinstance(config.pagination, Pagination):
pagination_response = PaginationResponse(
total=mongo_result.count() if mongo_result else 0,
- **config.pagination.dict(),
+ **config.pagination.model_dump(),
)
if transformer is None:
@@ -1732,7 +1737,7 @@ class MongoReader(GeneralReader):
filtered, child_config, transformer
)
if pagination is not None:
- pagination_dict = pagination.dict()
+ pagination_dict = pagination.model_dump()
if pagination_dict.get('order_by', None) == 'mainfile':
pagination_dict['order_by'] = 'mainfile_path'
await _populate_result(
@@ -2403,7 +2408,7 @@ class FileSystemReader(GeneralReader):
if config.pagination is not None:
assert isinstance(config.pagination, RawDirPagination)
start: int = config.pagination.get_simple_index()
- pagination: dict = config.pagination.dict(exclude_none=True)
+ pagination: dict = config.pagination.model_dump(exclude_none=True)
else:
start = 0
pagination = dict(page=1, page_size=10, order='asc')
@@ -2710,9 +2715,9 @@ class ArchiveReader(ArchiveLikeReader):
if isinstance(value, RequestConfig):
# this is a leaf, resolve it according to the config
- await self._resolve(
- child(current_path=child_path, archive=child_archive), value
- )
+ child_node = child(current_path=child_path, archive=child_archive)
+ await self._resolve_figure(child_node, node, value)
+ await self._resolve(child_node, value)
elif isinstance(value, dict):
# this is a nested query, keep walking down the tree
async def __walk(__path, __archive):
@@ -2736,6 +2741,48 @@ class ArchiveReader(ArchiveLikeReader):
# should never reach here
raise ConfigError(f'Invalid required config: {value}.')
+ @staticmethod
+ async def _resolve_figure(
+ child: GraphNode, parent: GraphNode, config: RequestConfig
+ ):
+ """
+ Ensure a Figure object is properly resolved.
+ """
+ if not isinstance(
+ child.definition, SubSection
+ ) or not child.definition.sub_section.m_follows(
+ PlotlyFigure.m_def, self_as_definition=True
+ ):
+ return
+
+ if config.directive is not DirectiveType.resolved:
+ return
+
+ async def _visit(_node):
+ if isinstance(_node, GenericDict):
+ for v in _node.values():
+ await _visit(v)
+ elif isinstance(_node, GenericList):
+ if len(_node) > 0 and isinstance(_node[0], int | float):
+ # looks like a data array
+ return
+ for v in _node:
+ await _visit(v)
+ elif isinstance(_node, str):
+ _node = [x for x in _node.lstrip('#').split('/') if x]
+ if _node and await _if_exists(parent.archive, _node):
+ await _populate_result(
+ parent.result_root,
+ parent.current_path + _node,
+ await _goto_path(parent.archive, _node),
+ )
+
+ if not isinstance(child.archive, GenericList):
+ return await _visit(child.archive)
+
+ for i in _normalise_index(config.index, len(child.archive)):
+ await _visit(child.archive[i])
+
async def _resolve(
self,
node: GraphNode,
@@ -2852,6 +2899,7 @@ class ArchiveReader(ArchiveLikeReader):
node.result_root, child_node.current_path, child_node.archive
)
else:
+ await self._resolve_figure(child_node, node, child_config)
await self._resolve(child_node, child_config)
async def _check_definition(
@@ -3418,7 +3466,7 @@ class MetainfoBrowser(DefinitionReader):
# we use the class member to cache the response
# it will be written to the result tree later
# we do not direct perform writing here to avoid turning all methods async
- self._pagination_response = default_pagination.dict()
+ self._pagination_response = default_pagination.model_dump()
self._pagination_response['total'] = total
return all_keys
diff --git a/nomad/metainfo/metainfo.py b/nomad/metainfo/metainfo.py
index 4ab86f86ffb5ec5fd9ffe45d74b15a00d786b8b8..c6deb3a24fe1d294f17925b924f322a23da80ea3 100644
--- a/nomad/metainfo/metainfo.py
+++ b/nomad/metainfo/metainfo.py
@@ -1776,13 +1776,24 @@ class MSection(metaclass=MObjectMeta):
# todo: mypy bug https://github.com/python/mypy/issues/14458
return cast(cls, self) # type: ignore
- def m_follows(self, definition: Section) -> bool:
+ def m_follows(
+ self, definition: Section, *, self_as_definition: bool = False
+ ) -> bool:
"""
Determines if this section's definition is or is derived from the given definition.
+
+ Arguments:
+ definition: The definition to check against.
+ self_as_definition: If True, the current section is considered as a definition
+ instead of a data section. This is useful when directly checking the definitions
+ without the need to create a dummy data section.
"""
if not isinstance(definition, Section):
raise TypeError(f'{definition} is not an instance of class Section.')
- return definition in itertools.chain(self.m_def.all_base_sections, [self.m_def])
+
+ target = self if self_as_definition else self.m_def
+
+ return definition in itertools.chain(target.all_base_sections, [target])
def m_to_dict(
self,
diff --git a/nomad/utils/exampledata.py b/nomad/utils/exampledata.py
index 4603a39b65b32d6c9e5afa016c34e1ed1275981d..8778de74a5b5885a0af8f3ee04024cded81273a3 100644
--- a/nomad/utils/exampledata.py
+++ b/nomad/utils/exampledata.py
@@ -328,7 +328,11 @@ class ExampleData:
if archive is not None:
entry_archive.m_update(**archive)
- if entry_archive.results.material.material_id is None:
+ if (
+ entry_archive.results
+ and entry_archive.results.material
+ and entry_archive.results.material.material_id is None
+ ):
entry_archive.results.material.material_id = material_id
self.archives[entry_id] = entry_archive
diff --git a/tests/graph/test_graph_reader.py b/tests/graph/test_graph_reader.py
index ad033aec9c837fda3d1e9f9784d4b8a750f62803..946d196ba39c17d8c585d7240d6366c3e5bc9cf8 100644
--- a/tests/graph/test_graph_reader.py
+++ b/tests/graph/test_graph_reader.py
@@ -34,7 +34,7 @@ from nomad.graph.graph_reader import (
)
from nomad.graph.lazy_wrapper import LazyWrapper
from nomad.utils.exampledata import ExampleData
-from tests.normalizing.conftest import simulationworkflowschema
+from tests.normalizing.conftest import run_processing, simulationworkflowschema
from tests.utils import ListWithSortKey
@@ -4034,3 +4034,113 @@ def json_dict():
'results': {'calculation_result_ref': '/run/0/calculation/1'},
},
}
+
+
+@pytest.fixture(scope='function')
+def example_data_with_figure(proc_infra, user1):
+ data = ExampleData(main_author=user1)
+
+ data.create_upload(
+ upload_id='id_published_with_ref', upload_name='name_published', published=False
+ )
+
+ directory = 'tests/data/datamodel/metainfo/plotly'
+ mainfile = 'plotly.schema.archive.yaml'
+ data.create_entry(
+ upload_id='id_published_with_ref',
+ entry_id='id_plotly',
+ entry_archive=run_processing(directory, mainfile),
+ )
+
+ for archive in data.archives.values():
+ archive.metadata.apply_archive_metadata(archive)
+
+ data.save(with_files=True, with_es=True, with_mongo=True)
+
+ yield data
+
+ data.delete()
+
+
+@pytest.mark.parametrize(
+ 'query,result',
+ [
+ # plain get default quantities
+ # the references are not resolved
+ pytest.param(
+ {
+ Token.ARCHIVE: {
+ 'data': {
+ 'figures[0]': {
+ 'm_request': {
+ 'directive': 'plain',
+ },
+ }
+ }
+ },
+ },
+ {
+ 'archive': {
+ 'data': {
+ 'figures': [
+ {
+ 'label': 'graph object 1',
+ 'figure': {
+ 'data': {'x': '#xArr', 'y': '#xArr'},
+ 'layout': {
+ 'title': {'text': 'Plot in section level'},
+ 'xaxis': {'title': {'text': 'x data'}},
+ 'yaxis': {'title': {'text': 'y data'}},
+ },
+ },
+ }
+ ]
+ }
+ }
+ },
+ id='plain-read',
+ ),
+ pytest.param(
+ {
+ Token.ARCHIVE: {
+ 'data': {
+ 'figures[0]': {
+ 'm_request': {
+ 'directive': 'resolved',
+ },
+ }
+ }
+ },
+ },
+ {
+ 'archive': {
+ 'data': {
+ 'xArr': [1.1, 2.0, 3.0, 4.0, 5.0],
+ 'figures': [
+ {
+ 'label': 'graph object 1',
+ 'figure': {
+ 'data': {'x': '#xArr', 'y': '#xArr'},
+ 'layout': {
+ 'title': {'text': 'Plot in section level'},
+ 'xaxis': {'title': {'text': 'x data'}},
+ 'yaxis': {'title': {'text': 'y data'}},
+ },
+ },
+ }
+ ],
+ }
+ }
+ },
+ id='read-resolved',
+ ),
+ ],
+)
+def test_figure_resolution(user1, example_data_with_figure, query, result):
+ def __entry_print(required, *, result=None):
+ with EntryReader(required, user=user1) as reader:
+ response = reader.sync_read('id_plotly')
+ if result:
+ assert_dict(response, result)
+
+ __entry_print(query, result=result)