From f2c3a5b7c9b40fe5b6ba1a01e9ca6cfeb3653bec Mon Sep 17 00:00:00 2001
From: Theodore Chang <tlcfem@gmail.com>
Date: Sun, 16 Mar 2025 22:34:32 +0100
Subject: [PATCH 01/12] Refactor response handling to use model_dump for
improved serialization
---
nomad/graph/graph_reader.py | 30 ++++++++++++++++++------------
1 file changed, 18 insertions(+), 12 deletions(-)
diff --git a/nomad/graph/graph_reader.py b/nomad/graph/graph_reader.py
index 84ee4b7f16..9d1900b3a4 100644
--- a/nomad/graph/graph_reader.py
+++ b/nomad/graph/graph_reader.py
@@ -424,7 +424,7 @@ 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 +989,7 @@ 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 +1026,7 @@ 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 +1334,7 @@ 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 +1391,9 @@ 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 +1426,9 @@ 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 +1452,9 @@ 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 +1463,7 @@ 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 +1479,7 @@ 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 +1738,7 @@ 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 +2409,7 @@ 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')
@@ -3418,7 +3424,7 @@ 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
--
GitLab
From 92c36e707a7a4667e6010b2387a4b6ac399635b5 Mon Sep 17 00:00:00 2001
From: Theodore Chang <tlcfem@gmail.com>
Date: Sun, 16 Mar 2025 17:53:48 +0100
Subject: [PATCH 02/12] Refactor graph path navigation methods and add figure
resolution support
---
nomad/graph/graph_reader.py | 65 ++++++++++++++++++++++++++++---------
1 file changed, 50 insertions(+), 15 deletions(-)
diff --git a/nomad/graph/graph_reader.py b/nomad/graph/graph_reader.py
index 9d1900b3a4..ac9fffb033 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:
@@ -2716,9 +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):
@@ -2742,6 +2741,41 @@ 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, PlotlyFigure):
+ 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):
+ for v in _node:
+ await _visit(v)
+ elif isinstance(_node, str):
+ _node = [x for x in _node.lstrip('#').split('/') if x]
+ if _node and _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,
@@ -2858,6 +2892,7 @@ 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(
--
GitLab
From 67776d6e34703ee4facb499566523dd9c3503bfc Mon Sep 17 00:00:00 2001
From: Theodore Chang <tlcfem@gmail.com>
Date: Tue, 18 Mar 2025 19:39:47 +0100
Subject: [PATCH 03/12] Refactor figure resolution check to use method
comparison for improved accuracy
---
nomad/graph/graph_reader.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/nomad/graph/graph_reader.py b/nomad/graph/graph_reader.py
index ac9fffb033..0974b886ac 100644
--- a/nomad/graph/graph_reader.py
+++ b/nomad/graph/graph_reader.py
@@ -2748,7 +2748,7 @@ class ArchiveReader(ArchiveLikeReader):
"""
Ensure a Figure object is properly resolved.
"""
- if not isinstance(child.definition, PlotlyFigure):
+ if not child.definition.m_follows(PlotlyFigure.m_def):
return
if config.directive is not DirectiveType.resolved:
--
GitLab
From b2b9df2434f94713a71bb79e77b7d5cd14911297 Mon Sep 17 00:00:00 2001
From: Theodore Chang <tlcfem@gmail.com>
Date: Thu, 20 Mar 2025 14:57:50 +0100
Subject: [PATCH 04/12] Refactor graph traversal to handle data arrays in
GenericList more effectively
---
nomad/graph/graph_reader.py | 3 +++
1 file changed, 3 insertions(+)
diff --git a/nomad/graph/graph_reader.py b/nomad/graph/graph_reader.py
index 0974b886ac..05de1f9e23 100644
--- a/nomad/graph/graph_reader.py
+++ b/nomad/graph/graph_reader.py
@@ -2759,6 +2759,9 @@ class ArchiveReader(ArchiveLikeReader):
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):
--
GitLab
From 692240a1533b8e823504330d79873eaca5aec647 Mon Sep 17 00:00:00 2001
From: mohammad <mohammad.nakhaee.1@gmail.com>
Date: Mon, 24 Mar 2025 17:26:59 +0100
Subject: [PATCH 05/12] added drafts for test figure
---
.../plotly/plotly_references.archive.json | 7629 +++++++++++++++++
tests/graph/test_graph_reader.py | 79 +
2 files changed, 7708 insertions(+)
create mode 100644 tests/data/datamodel/metainfo/plotly/plotly_references.archive.json
diff --git a/tests/data/datamodel/metainfo/plotly/plotly_references.archive.json b/tests/data/datamodel/metainfo/plotly/plotly_references.archive.json
new file mode 100644
index 0000000000..f24dcd42e4
--- /dev/null
+++ b/tests/data/datamodel/metainfo/plotly/plotly_references.archive.json
@@ -0,0 +1,7629 @@
+{
+ "processing_logs": [
+ {
+ "event": "Executing local process",
+ "proc": "Entry",
+ "process": "None",
+ "process_worker_id": "nL2iuGaYRVye8CSvPN9RMg",
+ "parser": "parsers/archive",
+ "logger": "nomad.processing",
+ "timestamp": "2025-03-19 18:42.21",
+ "level": "DEBUG"
+ },
+ {
+ "exec_time": "0.0010509490966796875",
+ "input_size": "78",
+ "event": "parser executed",
+ "proc": "Entry",
+ "process": "process_entry_local",
+ "process_worker_id": "nL2iuGaYRVye8CSvPN9RMg",
+ "parser": "parsers/archive",
+ "step": "parsers/archive",
+ "logger": "nomad.processing",
+ "timestamp": "2025-03-19 18:42.21",
+ "level": "INFO"
+ },
+ {
+ "normalizer": "MetainfoNormalizer",
+ "step": "MetainfoNormalizer",
+ "event": "normalizer completed successfully",
+ "proc": "Entry",
+ "process": "process_entry_local",
+ "process_worker_id": "nL2iuGaYRVye8CSvPN9RMg",
+ "parser": "parsers/archive",
+ "logger": "nomad.processing",
+ "timestamp": "2025-03-19 18:42.22",
+ "level": "INFO"
+ },
+ {
+ "exec_time": "0.32399463653564453",
+ "input_size": "78",
+ "event": "normalizer executed",
+ "proc": "Entry",
+ "process": "process_entry_local",
+ "process_worker_id": "nL2iuGaYRVye8CSvPN9RMg",
+ "parser": "parsers/archive",
+ "normalizer": "MetainfoNormalizer",
+ "step": "MetainfoNormalizer",
+ "logger": "nomad.processing",
+ "timestamp": "2025-03-19 18:42.22",
+ "level": "INFO"
+ },
+ {
+ "normalizer": "ResultsNormalizer",
+ "step": "ResultsNormalizer",
+ "event": "normalizer completed successfully",
+ "proc": "Entry",
+ "process": "process_entry_local",
+ "process_worker_id": "nL2iuGaYRVye8CSvPN9RMg",
+ "parser": "parsers/archive",
+ "logger": "nomad.processing",
+ "timestamp": "2025-03-19 18:42.22",
+ "level": "INFO"
+ },
+ {
+ "exec_time": "0.0004916191101074219",
+ "input_size": "78",
+ "event": "normalizer executed",
+ "proc": "Entry",
+ "process": "process_entry_local",
+ "process_worker_id": "nL2iuGaYRVye8CSvPN9RMg",
+ "parser": "parsers/archive",
+ "normalizer": "ResultsNormalizer",
+ "step": "ResultsNormalizer",
+ "logger": "nomad.processing",
+ "timestamp": "2025-03-19 18:42.22",
+ "level": "INFO"
+ },
+ {
+ "exec_time": "0.0041081905364990234",
+ "event": "entry metadata saved",
+ "proc": "Entry",
+ "process": "process_entry_local",
+ "process_worker_id": "nL2iuGaYRVye8CSvPN9RMg",
+ "parser": "parsers/archive",
+ "logger": "nomad.processing",
+ "timestamp": "2025-03-19 18:42.24",
+ "level": "INFO"
+ },
+ {
+ "exec_time": "0.01975393295288086",
+ "event": "entry metadata indexed",
+ "proc": "Entry",
+ "process": "process_entry_local",
+ "process_worker_id": "nL2iuGaYRVye8CSvPN9RMg",
+ "parser": "parsers/archive",
+ "logger": "nomad.processing",
+ "timestamp": "2025-03-19 18:42.24",
+ "level": "INFO"
+ }
+ ],
+ "data": {
+ "m_def": "nomad.datamodel.metainfo.testPlotlyGraphAPI.CustomSection",
+ "x": [
+ 0.0,
+ 1.0,
+ 2.0,
+ 3.0,
+ 4.0
+ ],
+ "y": [
+ -2.0,
+ -1.0,
+ 0.0,
+ 1.0,
+ 2.0
+ ],
+ "z": [
+ -2.0,
+ -1.0,
+ 0.0,
+ 1.0,
+ 2.0
+ ],
+ "heatmap": [
+ [
+ 0.0,
+ 1.0,
+ 2.0,
+ 3.0,
+ 4.0
+ ],
+ [
+ 1.0,
+ 2.0,
+ 3.0,
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+ 5.0
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+ 6.0,
+ 7.0
+ ],
+ [
+ 4.0,
+ 5.0,
+ 6.0,
+ 7.0,
+ 8.0
+ ]
+ ],
+ "colors": [
+ 1.0,
+ 2.0,
+ 3.0,
+ 4.0,
+ 5.0
+ ],
+ "sizes": [
+ 2.0,
+ 5.0,
+ 10.0,
+ 20.0,
+ 30.0
+ ],
+ "a": [
+ 0.0,
+ 0.0,
+ 0.0
+ ],
+ "b": [
+ 0.0,
+ 1.0,
+ 2.0
+ ],
+ "c": [
+ 0.0,
+ 0.0,
+ 0.0
+ ],
+ "u": [
+ 0.0,
+ 0.0,
+ 0.0
+ ],
+ "v": [
+ 1.0,
+ 1.0,
+ 1.0
+ ],
+ "w": [
+ 0.0,
+ 0.0,
+ 0.0
+ ],
+ "x3d": [
+ [
+ [
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+ -1.0,
+ -1.0,
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+ ],
+ [
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+ -1.0,
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+ "nomad_version": "1.3.16.dev121+g8289fdc4a",
+ "nomad_commit": "",
+ "nomad_distro_commit_url": "",
+ "references": [],
+ "main_author": "68878af7-6845-46c0-b2c1-250d4d8eb470",
+ "coauthors": [],
+ "coauthor_groups": [],
+ "entry_coauthors": [],
+ "reviewers": [],
+ "reviewer_groups": [],
+ "datasets": [],
+ "n_quantities": 80,
+ "quantities": [
+ "",
+ "data",
+ "data.a",
+ "data.b",
+ "data.c",
+ "data.cells",
+ "data.colors",
+ "data.figures",
+ "data.figures.figure",
+ "data.figures.label",
+ "data.header",
+ "data.heatmap",
+ "data.sizes",
+ "data.surf1",
+ "data.surf2",
+ "data.u",
+ "data.v",
+ "data.w",
+ "data.x",
+ "data.x3d",
+ "data.y",
+ "data.y3d",
+ "data.z",
+ "data.z3d",
+ "metadata",
+ "metadata.coauthor_groups",
+ "metadata.coauthors",
+ "metadata.datasets",
+ "metadata.embargo_length",
+ "metadata.entry_coauthors",
+ "metadata.entry_create_time",
+ "metadata.entry_hash",
+ "metadata.entry_id",
+ "metadata.entry_name",
+ "metadata.entry_timestamp",
+ "metadata.entry_timestamp.timestamp",
+ "metadata.entry_timestamp.token",
+ "metadata.entry_timestamp.token_seed",
+ "metadata.entry_timestamp.tsa_server",
+ "metadata.entry_type",
+ "metadata.files",
+ "metadata.last_processing_time",
+ "metadata.license",
+ "metadata.main_author",
+ "metadata.mainfile",
+ "metadata.nomad_commit",
+ "metadata.nomad_distro_commit_url",
+ "metadata.nomad_version",
+ "metadata.parser_name",
+ "metadata.processed",
+ "metadata.processing_errors",
+ "metadata.published",
+ "metadata.quantities",
+ "metadata.references",
+ "metadata.reviewer_groups",
+ "metadata.reviewers",
+ "metadata.section_defs",
+ "metadata.section_defs.definition_id",
+ "metadata.section_defs.definition_qualified_name",
+ "metadata.section_defs.used_directly",
+ "metadata.sections",
+ "metadata.upload_create_time",
+ "metadata.upload_id",
+ "metadata.with_embargo",
+ "results",
+ "results.properties"
+ ],
+ "sections": [
+ "nomad.datamodel.datamodel.EntryArchive",
+ "nomad.datamodel.datamodel.EntryMetadata",
+ "nomad.datamodel.datamodel.RFC3161Timestamp",
+ "nomad.datamodel.metainfo.plot.PlotlyFigure",
+ "nomad.datamodel.metainfo.testPlotlyGraphAPI.CustomSection",
+ "nomad.datamodel.results.Properties",
+ "nomad.datamodel.results.Results"
+ ],
+ "entry_timestamp": {
+ "token_seed": "umwDnLW6dlqL6ecIO67Lp-bAfCl4",
+ "token": "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",
+ "tsa_server": "http://zeitstempel.dfn.de",
+ "timestamp": "2025-03-19T17:42:21+00:00"
+ },
+ "section_defs": [
+ {
+ "definition_qualified_name": "nomad.datamodel.data.ArchiveSection",
+ "definition_id": "7047cbff9980abff17cce4b1b6b0d1c783505b7f",
+ "used_directly": true
+ },
+ {
+ "definition_qualified_name": "nomad.datamodel.data.EntryData",
+ "definition_id": "538f52fd8d52b29372066f878319c6aeb03b74d2",
+ "used_directly": true
+ },
+ {
+ "definition_qualified_name": "nomad.datamodel.datamodel.EntryArchive",
+ "definition_id": "f16d4e3a5dfc26fad085b5f636c0b18da32fc688",
+ "used_directly": true
+ },
+ {
+ "definition_qualified_name": "nomad.datamodel.datamodel.EntryMetadata",
+ "definition_id": "64204c5d96eb1385b547f3cb9148aa6d6a7c6f2a",
+ "used_directly": true
+ },
+ {
+ "definition_qualified_name": "nomad.datamodel.datamodel.RFC3161Timestamp",
+ "definition_id": "1e3e9dd7b802b04343f46305a7d0f58663d8110a",
+ "used_directly": true
+ },
+ {
+ "definition_qualified_name": "nomad.datamodel.metainfo.plot.Figure",
+ "definition_id": "bf82c8c5105b42f9390e7100b6206f55ecd75128",
+ "used_directly": true
+ },
+ {
+ "definition_qualified_name": "nomad.datamodel.metainfo.plot.PlotSection",
+ "definition_id": "7675be926f858e446639457fee3846873e9c4f1c",
+ "used_directly": true
+ },
+ {
+ "definition_qualified_name": "nomad.datamodel.metainfo.plot.PlotlyFigure",
+ "definition_id": "c2b92af9ee552c12ea402015d72cc227c5a5005e",
+ "used_directly": true
+ },
+ {
+ "definition_qualified_name": "nomad.datamodel.metainfo.testPlotlyGraphAPI.CustomSection",
+ "definition_id": "23c90a61eb30e91393791602d2fb4ba4b382bcbe",
+ "used_directly": true
+ },
+ {
+ "definition_qualified_name": "nomad.datamodel.results.Properties",
+ "definition_id": "9fcb2f8dea93e927ad23e6c6c43b732406796328",
+ "used_directly": true
+ },
+ {
+ "definition_qualified_name": "nomad.datamodel.results.Results",
+ "definition_id": "5ccde651cb447bc26cb8d44b37c08b78b725909e",
+ "used_directly": true
+ }
+ ],
+ "search_quantities": [
+ {
+ "id": "data.figures.label#nomad.datamodel.metainfo.testPlotlyGraphAPI.CustomSection",
+ "definition": "nomad.datamodel.metainfo.plot.Figure.label",
+ "path_archive": "data.figures.0.label",
+ "str_value": "figure 1"
+ },
+ {
+ "id": "data.figures.label#nomad.datamodel.metainfo.testPlotlyGraphAPI.CustomSection",
+ "definition": "nomad.datamodel.metainfo.plot.Figure.label",
+ "path_archive": "data.figures.1.label",
+ "str_value": "figure 2"
+ },
+ {
+ "id": "data.figures.label#nomad.datamodel.metainfo.testPlotlyGraphAPI.CustomSection",
+ "definition": "nomad.datamodel.metainfo.plot.Figure.label",
+ "path_archive": "data.figures.2.label",
+ "str_value": "figure 3"
+ },
+ {
+ "id": "data.figures.label#nomad.datamodel.metainfo.testPlotlyGraphAPI.CustomSection",
+ "definition": "nomad.datamodel.metainfo.plot.Figure.label",
+ "path_archive": "data.figures.3.label",
+ "str_value": "figure 4"
+ },
+ {
+ "id": "data.figures.label#nomad.datamodel.metainfo.testPlotlyGraphAPI.CustomSection",
+ "definition": "nomad.datamodel.metainfo.plot.Figure.label",
+ "path_archive": "data.figures.4.label",
+ "str_value": "figure 5"
+ },
+ {
+ "id": "data.figures.label#nomad.datamodel.metainfo.testPlotlyGraphAPI.CustomSection",
+ "definition": "nomad.datamodel.metainfo.plot.Figure.label",
+ "path_archive": "data.figures.5.label",
+ "str_value": "figure 6"
+ },
+ {
+ "id": "data.figures.label#nomad.datamodel.metainfo.testPlotlyGraphAPI.CustomSection",
+ "definition": "nomad.datamodel.metainfo.plot.Figure.label",
+ "path_archive": "data.figures.6.label",
+ "str_value": "figure 7"
+ },
+ {
+ "id": "data.figures.label#nomad.datamodel.metainfo.testPlotlyGraphAPI.CustomSection",
+ "definition": "nomad.datamodel.metainfo.plot.Figure.label",
+ "path_archive": "data.figures.7.label",
+ "str_value": "figure 9"
+ }
+ ]
+ },
+ "results": {
+ "properties": {}
+ },
+ "m_ref_archives": {}
+}
diff --git a/tests/graph/test_graph_reader.py b/tests/graph/test_graph_reader.py
index ad033aec9c..b7bb5cd8ba 100644
--- a/tests/graph/test_graph_reader.py
+++ b/tests/graph/test_graph_reader.py
@@ -36,6 +36,7 @@ from nomad.graph.lazy_wrapper import LazyWrapper
from nomad.utils.exampledata import ExampleData
from tests.normalizing.conftest import simulationworkflowschema
from tests.utils import ListWithSortKey
+from tests.normalizing.conftest import run_processing
def rprint(msg):
@@ -2725,6 +2726,51 @@ def test_general_reader(json_dict, example_data_with_reference, user1):
)
+# noinspection DuplicatedCode,SpellCheckingInspection
+def test_figure(json_dict, example_data_with_figure, user1):
+ def __ge_print(msg, required, *, to_file: bool = False, result: dict = None):
+ with MongoReader(required, user=user1) as reader:
+ if result:
+ assert_dict(reader.sync_read(), result)
+ else:
+ rprint(f'\n\nExample: {next(counter)} -> {msg}:')
+ rprint(required)
+ if not to_file:
+ rprint('output:')
+ rprint(reader.sync_read())
+ else:
+ with open('archive_reader_test.json', 'w') as f:
+ f.write(json.dumps(reader.sync_read()))
+
+ __ge_print(
+ 'general start from entry',
+ {
+ Token.ENTRIES: {
+ 'm_request': {
+ 'directive': 'resolved',
+ },
+ }
+ },
+ result={
+ Token.ENTRIES: {
+ 'id_plotly': {
+ 'process_running': False,
+ 'current_process': None,
+ 'process_status': 'SUCCESS',
+ 'last_status_message': None,
+ 'errors': [],
+ 'warnings': [],
+ 'complete_time': None,
+ 'entry_id': 'id_plotly',
+ 'mainfile_key': None,
+ 'upload_id': 'id_published_with_ref',
+ 'parser_name': 'parsers/vasp',
+ },
+ }
+ },
+ )
+
+
# noinspection DuplicatedCode,SpellCheckingInspection
def test_metainfo_reader(mongo_infra, user1):
def __ge_print(msg, required, *, to_file: bool = False, result: dict = None):
@@ -3983,6 +4029,39 @@ def example_data_with_reference(
data.delete()
+@pytest.fixture(scope='function')
+def example_data_with_figure(
+ elastic_function, raw_files_module, mongo_function, user1, json_dict
+):
+ """
+ Provides a couple of entries with references.
+
+ Only used in test_required_reader_with_remote_reference.
+ """
+ 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_references.archive.json'
+ plotly_archive = run_processing(directory, mainfile)
+ data.create_entry(
+ upload_id='id_published_with_ref',
+ entry_id=f'id_plotly',
+ entry_archive=EntryArchive.m_from_dict(plotly_archive),
+ )
+
+ 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.fixture(scope='function')
def json_dict():
return {
--
GitLab
From 6ed21940fc213f8c50db41e6c70772a30c50d255 Mon Sep 17 00:00:00 2001
From: Theodore Chang <tlcfem@gmail.com>
Date: Mon, 24 Mar 2025 17:37:42 +0100
Subject: [PATCH 06/12] Refactor example data fixture for figure tests and add
test for figure resolution
---
tests/graph/test_graph_reader.py | 138 +++++++++++++------------------
1 file changed, 58 insertions(+), 80 deletions(-)
diff --git a/tests/graph/test_graph_reader.py b/tests/graph/test_graph_reader.py
index b7bb5cd8ba..21f1b91de5 100644
--- a/tests/graph/test_graph_reader.py
+++ b/tests/graph/test_graph_reader.py
@@ -34,9 +34,8 @@ 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
-from tests.normalizing.conftest import run_processing
def rprint(msg):
@@ -2726,51 +2725,6 @@ def test_general_reader(json_dict, example_data_with_reference, user1):
)
-# noinspection DuplicatedCode,SpellCheckingInspection
-def test_figure(json_dict, example_data_with_figure, user1):
- def __ge_print(msg, required, *, to_file: bool = False, result: dict = None):
- with MongoReader(required, user=user1) as reader:
- if result:
- assert_dict(reader.sync_read(), result)
- else:
- rprint(f'\n\nExample: {next(counter)} -> {msg}:')
- rprint(required)
- if not to_file:
- rprint('output:')
- rprint(reader.sync_read())
- else:
- with open('archive_reader_test.json', 'w') as f:
- f.write(json.dumps(reader.sync_read()))
-
- __ge_print(
- 'general start from entry',
- {
- Token.ENTRIES: {
- 'm_request': {
- 'directive': 'resolved',
- },
- }
- },
- result={
- Token.ENTRIES: {
- 'id_plotly': {
- 'process_running': False,
- 'current_process': None,
- 'process_status': 'SUCCESS',
- 'last_status_message': None,
- 'errors': [],
- 'warnings': [],
- 'complete_time': None,
- 'entry_id': 'id_plotly',
- 'mainfile_key': None,
- 'upload_id': 'id_published_with_ref',
- 'parser_name': 'parsers/vasp',
- },
- }
- },
- )
-
-
# noinspection DuplicatedCode,SpellCheckingInspection
def test_metainfo_reader(mongo_infra, user1):
def __ge_print(msg, required, *, to_file: bool = False, result: dict = None):
@@ -4029,39 +3983,6 @@ def example_data_with_reference(
data.delete()
-@pytest.fixture(scope='function')
-def example_data_with_figure(
- elastic_function, raw_files_module, mongo_function, user1, json_dict
-):
- """
- Provides a couple of entries with references.
-
- Only used in test_required_reader_with_remote_reference.
- """
- 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_references.archive.json'
- plotly_archive = run_processing(directory, mainfile)
- data.create_entry(
- upload_id='id_published_with_ref',
- entry_id=f'id_plotly',
- entry_archive=EntryArchive.m_from_dict(plotly_archive),
- )
-
- 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.fixture(scope='function')
def json_dict():
return {
@@ -4113,3 +4034,60 @@ def json_dict():
'results': {'calculation_result_ref': '/run/0/calculation/1'},
},
}
+
+
+@pytest.fixture(scope='function')
+def example_data_with_figure(elastic_function, raw_files_module, mongo_function, 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_references.archive.json'
+ plotly_archive = run_processing(directory, mainfile)
+ data.create_entry(
+ upload_id='id_published_with_ref',
+ entry_id='id_plotly',
+ entry_archive=EntryArchive.m_from_dict(plotly_archive),
+ )
+
+ 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()
+
+
+def test_figure_resolution(user1, example_data_with_figure):
+ def __entry_print(msg, required, *, to_file: bool = False, result: dict = None):
+ with EntryReader(required, user=user1) as reader:
+ response = reader.sync_read('id_plotly')
+ if result:
+ assert_dict(response, result)
+ else:
+ rprint(f'\n\nExample: {next(counter)} -> {msg}:')
+ rprint(required)
+ if not to_file:
+ rprint('output:')
+ rprint(response)
+ else:
+ with open('entry_reader_test.json', 'w') as f:
+ f.write(json.dumps(response))
+
+ __entry_print(
+ 'read plotly figure',
+ {
+ 'm_request': {
+ 'directive': 'plain',
+ },
+ Token.ARCHIVE: {
+ 'm_request': {
+ 'directive': 'plain',
+ }
+ },
+ },
+ )
--
GitLab
From 8152cf8c5e5cff84bfd5c39f1b16989ff79d8714 Mon Sep 17 00:00:00 2001
From: mohammad <mohammad.nakhaee.1@gmail.com>
Date: Mon, 24 Mar 2025 17:53:24 +0100
Subject: [PATCH 07/12] fixed the issue with the test archive
---
.../plotly/plotly_references.archive.json | 321 +-----------------
1 file changed, 3 insertions(+), 318 deletions(-)
diff --git a/tests/data/datamodel/metainfo/plotly/plotly_references.archive.json b/tests/data/datamodel/metainfo/plotly/plotly_references.archive.json
index f24dcd42e4..b856eb3484 100644
--- a/tests/data/datamodel/metainfo/plotly/plotly_references.archive.json
+++ b/tests/data/datamodel/metainfo/plotly/plotly_references.archive.json
@@ -202,324 +202,9 @@
0.0,
0.0
],
- "x3d": [
- [
- [
- -1.0,
- -1.0,
- -1.0,
- -1.0
- ],
- [
- -1.0,
- -1.0,
- -1.0,
- -1.0
- ],
- [
- -1.0,
- -1.0,
- -1.0,
- -1.0
- ],
- [
- -1.0,
- -1.0,
- -1.0,
- -1.0
- ]
- ],
- [
- [
- -0.33333333333333337,
- -0.33333333333333337,
- -0.33333333333333337,
- -0.33333333333333337
- ],
- [
- -0.33333333333333337,
- -0.33333333333333337,
- -0.33333333333333337,
- -0.33333333333333337
- ],
- [
- -0.33333333333333337,
- -0.33333333333333337,
- -0.33333333333333337,
- -0.33333333333333337
- ],
- [
- -0.33333333333333337,
- -0.33333333333333337,
- -0.33333333333333337,
- -0.33333333333333337
- ]
- ],
- [
- [
- 0.33333333333333326,
- 0.33333333333333326,
- 0.33333333333333326,
- 0.33333333333333326
- ],
- [
- 0.33333333333333326,
- 0.33333333333333326,
- 0.33333333333333326,
- 0.33333333333333326
- ],
- [
- 0.33333333333333326,
- 0.33333333333333326,
- 0.33333333333333326,
- 0.33333333333333326
- ],
- [
- 0.33333333333333326,
- 0.33333333333333326,
- 0.33333333333333326,
- 0.33333333333333326
- ]
- ],
- [
- [
- 1.0,
- 1.0,
- 1.0,
- 1.0
- ],
- [
- 1.0,
- 1.0,
- 1.0,
- 1.0
- ],
- [
- 1.0,
- 1.0,
- 1.0,
- 1.0
- ],
- [
- 1.0,
- 1.0,
- 1.0,
- 1.0
- ]
- ]
- ],
- "y3d": [
- [
- [
- -1.0,
- -1.0,
- -1.0,
- -1.0
- ],
- [
- -0.33333333333333337,
- -0.33333333333333337,
- -0.33333333333333337,
- -0.33333333333333337
- ],
- [
- 0.33333333333333326,
- 0.33333333333333326,
- 0.33333333333333326,
- 0.33333333333333326
- ],
- [
- 1.0,
- 1.0,
- 1.0,
- 1.0
- ]
- ],
- [
- [
- -1.0,
- -1.0,
- -1.0,
- -1.0
- ],
- [
- -0.33333333333333337,
- -0.33333333333333337,
- -0.33333333333333337,
- -0.33333333333333337
- ],
- [
- 0.33333333333333326,
- 0.33333333333333326,
- 0.33333333333333326,
- 0.33333333333333326
- ],
- [
- 1.0,
- 1.0,
- 1.0,
- 1.0
- ]
- ],
- [
- [
- -1.0,
- -1.0,
- -1.0,
- -1.0
- ],
- [
- -0.33333333333333337,
- -0.33333333333333337,
- -0.33333333333333337,
- -0.33333333333333337
- ],
- [
- 0.33333333333333326,
- 0.33333333333333326,
- 0.33333333333333326,
- 0.33333333333333326
- ],
- [
- 1.0,
- 1.0,
- 1.0,
- 1.0
- ]
- ],
- [
- [
- -1.0,
- -1.0,
- -1.0,
- -1.0
- ],
- [
- -0.33333333333333337,
- -0.33333333333333337,
- -0.33333333333333337,
- -0.33333333333333337
- ],
- [
- 0.33333333333333326,
- 0.33333333333333326,
- 0.33333333333333326,
- 0.33333333333333326
- ],
- [
- 1.0,
- 1.0,
- 1.0,
- 1.0
- ]
- ]
- ],
- "z3d": [
- [
- [
- -1.0,
- -0.33333333333333337,
- 0.33333333333333326,
- 1.0
- ],
- [
- -1.0,
- -0.33333333333333337,
- 0.33333333333333326,
- 1.0
- ],
- [
- -1.0,
- -0.33333333333333337,
- 0.33333333333333326,
- 1.0
- ],
- [
- -1.0,
- -0.33333333333333337,
- 0.33333333333333326,
- 1.0
- ]
- ],
- [
- [
- -1.0,
- -0.33333333333333337,
- 0.33333333333333326,
- 1.0
- ],
- [
- -1.0,
- -0.33333333333333337,
- 0.33333333333333326,
- 1.0
- ],
- [
- -1.0,
- -0.33333333333333337,
- 0.33333333333333326,
- 1.0
- ],
- [
- -1.0,
- -0.33333333333333337,
- 0.33333333333333326,
- 1.0
- ]
- ],
- [
- [
- -1.0,
- -0.33333333333333337,
- 0.33333333333333326,
- 1.0
- ],
- [
- -1.0,
- -0.33333333333333337,
- 0.33333333333333326,
- 1.0
- ],
- [
- -1.0,
- -0.33333333333333337,
- 0.33333333333333326,
- 1.0
- ],
- [
- -1.0,
- -0.33333333333333337,
- 0.33333333333333326,
- 1.0
- ]
- ],
- [
- [
- -1.0,
- -0.33333333333333337,
- 0.33333333333333326,
- 1.0
- ],
- [
- -1.0,
- -0.33333333333333337,
- 0.33333333333333326,
- 1.0
- ],
- [
- -1.0,
- -0.33333333333333337,
- 0.33333333333333326,
- 1.0
- ],
- [
- -1.0,
- -0.33333333333333337,
- 0.33333333333333326,
- 1.0
- ]
- ]
- ],
+ "x3d": [1.0, 1.0, 1.0, 1.0],
+ "y3d": [2.0, 2.0, 2.0, 2.0],
+ "z3d": [3.0, 3.0, 3.0, 3.0],
"surf1": [
[
4.0,
--
GitLab
From 4f13c76bb1c6fd63cd53f073fa49cd7f7d4a1bf6 Mon Sep 17 00:00:00 2001
From: mohammad <mohammad.nakhaee.1@gmail.com>
Date: Mon, 24 Mar 2025 19:43:34 +0100
Subject: [PATCH 08/12] removed CustomSection
---
.../plotly/plotly_references.archive.json | 61 +------------------
1 file changed, 3 insertions(+), 58 deletions(-)
diff --git a/tests/data/datamodel/metainfo/plotly/plotly_references.archive.json b/tests/data/datamodel/metainfo/plotly/plotly_references.archive.json
index b856eb3484..1a3deb60a8 100644
--- a/tests/data/datamodel/metainfo/plotly/plotly_references.archive.json
+++ b/tests/data/datamodel/metainfo/plotly/plotly_references.archive.json
@@ -99,7 +99,7 @@
}
],
"data": {
- "m_def": "nomad.datamodel.metainfo.testPlotlyGraphAPI.CustomSection",
+ "m_def": "nomad.datamodel.data.EntryData",
"x": [
0.0,
1.0,
@@ -7077,7 +7077,7 @@
"upload_create_time": "2025-03-19T17:42:11.062000+00:00",
"entry_id": "ujku7LPDc-8aid-el-40AXLC8Fw_",
"entry_name": "a.archive.json",
- "entry_type": "CustomSection",
+ "entry_type": "EntryData",
"entry_hash": "umwDnLW6dlqL6ecIO67Lp-bAfCl4",
"entry_create_time": "2025-03-19T17:42:21.685000+00:00",
"parser_name": "parsers/archive",
@@ -7189,7 +7189,6 @@
"nomad.datamodel.datamodel.EntryMetadata",
"nomad.datamodel.datamodel.RFC3161Timestamp",
"nomad.datamodel.metainfo.plot.PlotlyFigure",
- "nomad.datamodel.metainfo.testPlotlyGraphAPI.CustomSection",
"nomad.datamodel.results.Properties",
"nomad.datamodel.results.Results"
],
@@ -7240,11 +7239,6 @@
"definition_id": "c2b92af9ee552c12ea402015d72cc227c5a5005e",
"used_directly": true
},
- {
- "definition_qualified_name": "nomad.datamodel.metainfo.testPlotlyGraphAPI.CustomSection",
- "definition_id": "23c90a61eb30e91393791602d2fb4ba4b382bcbe",
- "used_directly": true
- },
{
"definition_qualified_name": "nomad.datamodel.results.Properties",
"definition_id": "9fcb2f8dea93e927ad23e6c6c43b732406796328",
@@ -7256,56 +7250,7 @@
"used_directly": true
}
],
- "search_quantities": [
- {
- "id": "data.figures.label#nomad.datamodel.metainfo.testPlotlyGraphAPI.CustomSection",
- "definition": "nomad.datamodel.metainfo.plot.Figure.label",
- "path_archive": "data.figures.0.label",
- "str_value": "figure 1"
- },
- {
- "id": "data.figures.label#nomad.datamodel.metainfo.testPlotlyGraphAPI.CustomSection",
- "definition": "nomad.datamodel.metainfo.plot.Figure.label",
- "path_archive": "data.figures.1.label",
- "str_value": "figure 2"
- },
- {
- "id": "data.figures.label#nomad.datamodel.metainfo.testPlotlyGraphAPI.CustomSection",
- "definition": "nomad.datamodel.metainfo.plot.Figure.label",
- "path_archive": "data.figures.2.label",
- "str_value": "figure 3"
- },
- {
- "id": "data.figures.label#nomad.datamodel.metainfo.testPlotlyGraphAPI.CustomSection",
- "definition": "nomad.datamodel.metainfo.plot.Figure.label",
- "path_archive": "data.figures.3.label",
- "str_value": "figure 4"
- },
- {
- "id": "data.figures.label#nomad.datamodel.metainfo.testPlotlyGraphAPI.CustomSection",
- "definition": "nomad.datamodel.metainfo.plot.Figure.label",
- "path_archive": "data.figures.4.label",
- "str_value": "figure 5"
- },
- {
- "id": "data.figures.label#nomad.datamodel.metainfo.testPlotlyGraphAPI.CustomSection",
- "definition": "nomad.datamodel.metainfo.plot.Figure.label",
- "path_archive": "data.figures.5.label",
- "str_value": "figure 6"
- },
- {
- "id": "data.figures.label#nomad.datamodel.metainfo.testPlotlyGraphAPI.CustomSection",
- "definition": "nomad.datamodel.metainfo.plot.Figure.label",
- "path_archive": "data.figures.6.label",
- "str_value": "figure 7"
- },
- {
- "id": "data.figures.label#nomad.datamodel.metainfo.testPlotlyGraphAPI.CustomSection",
- "definition": "nomad.datamodel.metainfo.plot.Figure.label",
- "path_archive": "data.figures.7.label",
- "str_value": "figure 9"
- }
- ]
+ "search_quantities": []
},
"results": {
"properties": {}
--
GitLab
From 936d63e71e96f7f09bb5cfb952af0ad2bfce2db0 Mon Sep 17 00:00:00 2001
From: Theodore Chang <tlcfem@gmail.com>
Date: Mon, 24 Mar 2025 20:12:14 +0100
Subject: [PATCH 09/12] Refactor entry archive material ID assignment and
update plotly archive processing
---
nomad/utils/exampledata.py | 6 +++++-
tests/graph/test_graph_reader.py | 16 ++++++++--------
2 files changed, 13 insertions(+), 9 deletions(-)
diff --git a/nomad/utils/exampledata.py b/nomad/utils/exampledata.py
index 4603a39b65..8778de74a5 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 21f1b91de5..e6c23100f8 100644
--- a/tests/graph/test_graph_reader.py
+++ b/tests/graph/test_graph_reader.py
@@ -4045,12 +4045,11 @@ def example_data_with_figure(elastic_function, raw_files_module, mongo_function,
)
directory = 'tests/data/datamodel/metainfo/plotly'
- mainfile = 'plotly_references.archive.json'
- plotly_archive = run_processing(directory, mainfile)
+ mainfile = 'plotly.schema.archive.yaml'
data.create_entry(
upload_id='id_published_with_ref',
entry_id='id_plotly',
- entry_archive=EntryArchive.m_from_dict(plotly_archive),
+ entry_archive=run_processing(directory, mainfile),
)
for archive in data.archives.values():
@@ -4081,12 +4080,13 @@ def test_figure_resolution(user1, example_data_with_figure):
__entry_print(
'read plotly figure',
{
- 'm_request': {
- 'directive': 'plain',
- },
Token.ARCHIVE: {
- 'm_request': {
- 'directive': 'plain',
+ 'data': {
+ 'figures[0]': {
+ 'm_request': {
+ 'directive': 'resolved',
+ },
+ }
}
},
},
--
GitLab
From 9e41e73195b8554d1909fc6c06c78bff903795db Mon Sep 17 00:00:00 2001
From: Theodore Chang <tlcfem@gmail.com>
Date: Mon, 24 Mar 2025 20:52:57 +0100
Subject: [PATCH 10/12] Refactor m_follows method to support self-as-definition
check and update figure resolution handling
---
nomad/graph/graph_reader.py | 8 ++++++--
nomad/metainfo/metainfo.py | 14 +++++++++++++-
2 files changed, 19 insertions(+), 3 deletions(-)
diff --git a/nomad/graph/graph_reader.py b/nomad/graph/graph_reader.py
index 05de1f9e23..cdf50b86c4 100644
--- a/nomad/graph/graph_reader.py
+++ b/nomad/graph/graph_reader.py
@@ -2748,7 +2748,11 @@ class ArchiveReader(ArchiveLikeReader):
"""
Ensure a Figure object is properly resolved.
"""
- if not child.definition.m_follows(PlotlyFigure.m_def):
+ 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:
@@ -2766,7 +2770,7 @@ class ArchiveReader(ArchiveLikeReader):
await _visit(v)
elif isinstance(_node, str):
_node = [x for x in _node.lstrip('#').split('/') if x]
- if _node and _if_exists(parent.archive, _node):
+ if _node and await _if_exists(parent.archive, _node):
await _populate_result(
parent.result_root,
parent.current_path + _node,
diff --git a/nomad/metainfo/metainfo.py b/nomad/metainfo/metainfo.py
index 074d3ce6ca..93b68c70a4 100644
--- a/nomad/metainfo/metainfo.py
+++ b/nomad/metainfo/metainfo.py
@@ -1779,12 +1779,24 @@ 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.')
+
+ if self_as_definition:
+ return definition in itertools.chain(self.all_base_sections, [self])
+
return definition in itertools.chain(self.m_def.all_base_sections, [self.m_def])
def m_to_dict(
--
GitLab
From f5e5d44c1e709a29f6c710490f6802a5b67f71e5 Mon Sep 17 00:00:00 2001
From: Theodore Chang <tlcfem@gmail.com>
Date: Thu, 27 Mar 2025 00:01:55 +0100
Subject: [PATCH 11/12] Refactor test_figure_resolution to use parameterized
tests and simplify example data fixture
---
tests/graph/test_graph_reader.py | 105 +++++++++++++++++++++++--------
1 file changed, 79 insertions(+), 26 deletions(-)
diff --git a/tests/graph/test_graph_reader.py b/tests/graph/test_graph_reader.py
index e6c23100f8..946d196ba3 100644
--- a/tests/graph/test_graph_reader.py
+++ b/tests/graph/test_graph_reader.py
@@ -4037,7 +4037,7 @@ def json_dict():
@pytest.fixture(scope='function')
-def example_data_with_figure(elastic_function, raw_files_module, mongo_function, user1):
+def example_data_with_figure(proc_infra, user1):
data = ExampleData(main_author=user1)
data.create_upload(
@@ -4058,36 +4058,89 @@ def example_data_with_figure(elastic_function, raw_files_module, mongo_function,
data.save(with_files=True, with_es=True, with_mongo=True)
yield data
+
data.delete()
-def test_figure_resolution(user1, example_data_with_figure):
- def __entry_print(msg, required, *, to_file: bool = False, result: dict = None):
+@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)
- else:
- rprint(f'\n\nExample: {next(counter)} -> {msg}:')
- rprint(required)
- if not to_file:
- rprint('output:')
- rprint(response)
- else:
- with open('entry_reader_test.json', 'w') as f:
- f.write(json.dumps(response))
- __entry_print(
- 'read plotly figure',
- {
- Token.ARCHIVE: {
- 'data': {
- 'figures[0]': {
- 'm_request': {
- 'directive': 'resolved',
- },
- }
- }
- },
- },
- )
+ __entry_print(query, result=result)
--
GitLab
From 3491e143cec591b1e7aa85c66ac256e0de7cd03a Mon Sep 17 00:00:00 2001
From: Theodore Chang <tlcfem@gmail.com>
Date: Thu, 27 Mar 2025 00:04:52 +0100
Subject: [PATCH 12/12] Refactor m_follows method to improve self-as-definition
handling and simplify section checks
---
nomad/metainfo/metainfo.py | 5 +-
.../plotly/plotly_references.archive.json | 7259 -----------------
2 files changed, 2 insertions(+), 7262 deletions(-)
delete mode 100644 tests/data/datamodel/metainfo/plotly/plotly_references.archive.json
diff --git a/nomad/metainfo/metainfo.py b/nomad/metainfo/metainfo.py
index 93b68c70a4..fdd8201768 100644
--- a/nomad/metainfo/metainfo.py
+++ b/nomad/metainfo/metainfo.py
@@ -1794,10 +1794,9 @@ class MSection(metaclass=MObjectMeta):
if not isinstance(definition, Section):
raise TypeError(f'{definition} is not an instance of class Section.')
- if self_as_definition:
- return definition in itertools.chain(self.all_base_sections, [self])
+ target = self if self_as_definition else self.m_def
- return definition in itertools.chain(self.m_def.all_base_sections, [self.m_def])
+ return definition in itertools.chain(target.all_base_sections, [target])
def m_to_dict(
self,
diff --git a/tests/data/datamodel/metainfo/plotly/plotly_references.archive.json b/tests/data/datamodel/metainfo/plotly/plotly_references.archive.json
deleted file mode 100644
index 1a3deb60a8..0000000000
--- a/tests/data/datamodel/metainfo/plotly/plotly_references.archive.json
+++ /dev/null
@@ -1,7259 +0,0 @@
-{
- "processing_logs": [
- {
- "event": "Executing local process",
- "proc": "Entry",
- "process": "None",
- "process_worker_id": "nL2iuGaYRVye8CSvPN9RMg",
- "parser": "parsers/archive",
- "logger": "nomad.processing",
- "timestamp": "2025-03-19 18:42.21",
- "level": "DEBUG"
- },
- {
- "exec_time": "0.0010509490966796875",
- "input_size": "78",
- "event": "parser executed",
- "proc": "Entry",
- "process": "process_entry_local",
- "process_worker_id": "nL2iuGaYRVye8CSvPN9RMg",
- "parser": "parsers/archive",
- "step": "parsers/archive",
- "logger": "nomad.processing",
- "timestamp": "2025-03-19 18:42.21",
- "level": "INFO"
- },
- {
- "normalizer": "MetainfoNormalizer",
- "step": "MetainfoNormalizer",
- "event": "normalizer completed successfully",
- "proc": "Entry",
- "process": "process_entry_local",
- "process_worker_id": "nL2iuGaYRVye8CSvPN9RMg",
- "parser": "parsers/archive",
- "logger": "nomad.processing",
- "timestamp": "2025-03-19 18:42.22",
- "level": "INFO"
- },
- {
- "exec_time": "0.32399463653564453",
- "input_size": "78",
- "event": "normalizer executed",
- "proc": "Entry",
- "process": "process_entry_local",
- "process_worker_id": "nL2iuGaYRVye8CSvPN9RMg",
- "parser": "parsers/archive",
- "normalizer": "MetainfoNormalizer",
- "step": "MetainfoNormalizer",
- "logger": "nomad.processing",
- "timestamp": "2025-03-19 18:42.22",
- "level": "INFO"
- },
- {
- "normalizer": "ResultsNormalizer",
- "step": "ResultsNormalizer",
- "event": "normalizer completed successfully",
- "proc": "Entry",
- "process": "process_entry_local",
- "process_worker_id": "nL2iuGaYRVye8CSvPN9RMg",
- "parser": "parsers/archive",
- "logger": "nomad.processing",
- "timestamp": "2025-03-19 18:42.22",
- "level": "INFO"
- },
- {
- "exec_time": "0.0004916191101074219",
- "input_size": "78",
- "event": "normalizer executed",
- "proc": "Entry",
- "process": "process_entry_local",
- "process_worker_id": "nL2iuGaYRVye8CSvPN9RMg",
- "parser": "parsers/archive",
- "normalizer": "ResultsNormalizer",
- "step": "ResultsNormalizer",
- "logger": "nomad.processing",
- "timestamp": "2025-03-19 18:42.22",
- "level": "INFO"
- },
- {
- "exec_time": "0.0041081905364990234",
- "event": "entry metadata saved",
- "proc": "Entry",
- "process": "process_entry_local",
- "process_worker_id": "nL2iuGaYRVye8CSvPN9RMg",
- "parser": "parsers/archive",
- "logger": "nomad.processing",
- "timestamp": "2025-03-19 18:42.24",
- "level": "INFO"
- },
- {
- "exec_time": "0.01975393295288086",
- "event": "entry metadata indexed",
- "proc": "Entry",
- "process": "process_entry_local",
- "process_worker_id": "nL2iuGaYRVye8CSvPN9RMg",
- "parser": "parsers/archive",
- "logger": "nomad.processing",
- "timestamp": "2025-03-19 18:42.24",
- "level": "INFO"
- }
- ],
- "data": {
- "m_def": "nomad.datamodel.data.EntryData",
- "x": [
- 0.0,
- 1.0,
- 2.0,
- 3.0,
- 4.0
- ],
- "y": [
- -2.0,
- -1.0,
- 0.0,
- 1.0,
- 2.0
- ],
- "z": [
- -2.0,
- -1.0,
- 0.0,
- 1.0,
- 2.0
- ],
- "heatmap": [
- [
- 0.0,
- 1.0,
- 2.0,
- 3.0,
- 4.0
- ],
- [
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GitLab