Automated dependency upgrades

LICENSE

@@ -1,4 +1,4 @@
-maggma Copyright (c) 2017, The Regents of the University of
+Copyright (c) 2017, The Regents of the University of
 California, through Lawrence Berkeley National Laboratory (subject
 to receipt of any required approvals from the U.S. Dept. of Energy).
 All rights reserved.

mp_api/client/core/client.py

@@ -7,7 +7,6 @@
 
 import inspect
 import itertools
-import json
 import os
 import platform
 import sys
@@ -29,9 +28,7 @@
 from urllib.parse import quote, urljoin
 
 import requests
-from bson import json_util
 from emmet.core.utils import jsanitize
-from monty.json import MontyDecoder
 from pydantic import BaseModel, create_model
 from requests.adapters import HTTPAdapter
 from requests.exceptions import RequestException
@@ -40,7 +37,7 @@
 from urllib3.util.retry import Retry
 
 from mp_api.client.core.settings import MAPIClientSettings
-from mp_api.client.core.utils import api_sanitize, validate_ids
+from mp_api.client.core.utils import api_sanitize, load_json, validate_ids
 
 try:
     import boto3
@@ -270,11 +267,7 @@ def _post_resource(
             response = self.session.post(url, json=payload, verify=True, params=params)
 
             if response.status_code == 200:
-                if self.monty_decode:
-                    data = json.loads(response.text, cls=MontyDecoder)
-                else:
-                    data = json.loads(response.text)
-
+                data = load_json(response.text, deser=self.monty_decode)
                 if self.document_model and use_document_model:
                     if isinstance(data["data"], dict):
                         data["data"] = self.document_model.model_validate(data["data"])  # type: ignore
@@ -287,7 +280,7 @@ def _post_resource(
 
             else:
                 try:
-                    data = json.loads(response.text)["detail"]
+                    data = load_json(response.text)["detail"]
                 except (JSONDecodeError, KeyError):
                     data = f"Response {response.text}"
                 if isinstance(data, str):
@@ -342,11 +335,7 @@ def _patch_resource(
             response = self.session.patch(url, json=payload, verify=True, params=params)
 
             if response.status_code == 200:
-                if self.monty_decode:
-                    data = json.loads(response.text, cls=MontyDecoder)
-                else:
-                    data = json.loads(response.text)
-
+                data = load_json(response.text, deser=self.monty_decode)
                 if self.document_model and use_document_model:
                     if isinstance(data["data"], dict):
                         data["data"] = self.document_model.model_validate(data["data"])  # type: ignore
@@ -359,7 +348,7 @@ def _patch_resource(
 
             else:
                 try:
-                    data = json.loads(response.text)["detail"]
+                    data = load_json(response.text)["detail"]
                 except (JSONDecodeError, KeyError):
                     data = f"Response {response.text}"
                 if isinstance(data, str):
@@ -384,18 +373,24 @@ def _query_open_data(
         self,
         bucket: str,
         key: str,
-        decoder: Callable,
+        decoder: Callable | None = None,
     ) -> tuple[list[dict] | list[bytes], int]:
         """Query and deserialize Materials Project AWS open data s3 buckets.
 
         Args:
             bucket (str): Materials project bucket name
             key (str): Key for file including all prefixes
-            decoder(Callable): Callable used to deserialize data
+            decoder(Callable or None): Callable used to deserialize data.
+                Defaults to mp_api.core.utils.load_json
 
         Returns:
             dict: MontyDecoded data
         """
+        if not decoder:
+
+            def decoder(x):
+                return load_json(x, deser=self.monty_decode)
+
         file = open(
             f"s3://{bucket}/{key}",
             encoding="utf-8",
@@ -527,16 +522,11 @@ def _query_resource(
                         "Ignoring `fields` argument: All fields are always included when no query is provided."
                     )
 
-                decoder = (
-                    MontyDecoder().decode if self.monty_decode else json_util.loads
-                )
-
                 # Multithreaded function inputs
                 s3_params_list = {
                     key: {
                         "bucket": bucket,
                         "key": key,
-                        "decoder": decoder,
                     }
                     for key in keys
                 }
@@ -1013,11 +1003,7 @@ def _submit_request_and_process(
             )
 
         if response.status_code == 200:
-            if self.monty_decode:
-                data = json.loads(response.text, cls=MontyDecoder)
-            else:
-                data = json.loads(response.text)
-
+            data = load_json(response.text, deser=self.monty_decode)
             # other sub-urls may use different document models
             # the client does not handle this in a particularly smart way currently
             if self.document_model and use_document_model:
@@ -1029,7 +1015,7 @@ def _submit_request_and_process(
 
         else:
             try:
-                data = json.loads(response.text)["detail"]
+                data = load_json(response.text)["detail"]
             except (JSONDecodeError, KeyError):
                 data = f"Response {response.text}"
             if isinstance(data, str):

mp_api/client/core/utils.py

@@ -4,15 +4,24 @@
 from functools import cache
 from typing import Optional, get_args
 
-from maggma.utils import get_flat_models_from_model
-from monty.json import MSONable
+import orjson
+from emmet.core.utils import get_flat_models_from_model
+from monty.json import MontyDecoder, MSONable
 from pydantic import BaseModel
 from pydantic._internal._utils import lenient_issubclass
 from pydantic.fields import FieldInfo
 
 from mp_api.client.core.settings import MAPIClientSettings
 
 
+def load_json(json_like: str | bytes, deser: bool = False, encoding: str = "utf-8"):
+    """Utility to load json in consistent manner."""
+    data = orjson.loads(
+        json_like if isinstance(json_like, bytes) else json_like.encode(encoding)
+    )
+    return MontyDecoder().process_decoded(data) if deser else data
+
+
 def validate_ids(id_list: list[str]):
     """Function to validate material and task IDs.
 

mp_api/client/mprester.py

@@ -1,11 +1,9 @@
 from __future__ import annotations
 
 import itertools
-import json
 import os
 import warnings
 from functools import cache, lru_cache
-from json import loads
 from typing import TYPE_CHECKING
 
 from emmet.core.electronic_structure import BSPathType
@@ -14,7 +12,6 @@
 from emmet.core.tasks import TaskDoc
 from emmet.core.thermo import ThermoType
 from emmet.core.vasp.calc_types import CalcType
-from monty.json import MontyDecoder
 from packaging import version
 from pymatgen.analysis.phase_diagram import PhaseDiagram
 from pymatgen.analysis.pourbaix_diagram import IonEntry
@@ -27,14 +24,15 @@
 
 from mp_api.client.core import BaseRester, MPRestError
 from mp_api.client.core.settings import MAPIClientSettings
-from mp_api.client.core.utils import validate_ids
+from mp_api.client.core.utils import load_json, validate_ids
 from mp_api.client.routes import GeneralStoreRester, MessagesRester, UserSettingsRester
 from mp_api.client.routes.materials import (
     AbsorptionRester,
     AlloysRester,
     BandStructureRester,
     BondsRester,
     ChemenvRester,
+    ConversionElectrodeRester,
     DielectricRester,
     DOIRester,
     DosRester,
@@ -99,6 +97,7 @@ class MPRester:
     robocrys: RobocrysRester
     synthesis: SynthesisRester
     insertion_electrodes: ElectrodeRester
+    conversion_electrodes: ConversionElectrodeRester
     electronic_structure: ElectronicStructureRester
     electronic_structure_bandstructure: BandStructureRester
     electronic_structure_dos: DosRester
@@ -1338,11 +1337,10 @@ def get_charge_density_from_task_id(
         Returns:
             (Chgcar, (Chgcar, TaskDoc | dict), None): Pymatgen Chgcar object, or tuple with object and TaskDoc
         """
-        decoder = MontyDecoder().decode if self.monty_decode else json.loads
         kwargs = dict(
             bucket="materialsproject-parsed",
             key=f"chgcars/{str(task_id)}.json.gz",
-            decoder=decoder,
+            decoder=lambda x: load_json(x, deser=self.monty_decode),
         )
         chgcar = self.materials.tasks._query_open_data(**kwargs)[0]
         if not chgcar:
@@ -1476,7 +1474,7 @@ def _check_nomad_exist(url) -> bool:
         response = get(url=url)
         if response.status_code != 200:
             return False
-        content = loads(response.text)
+        content = load_json(response.text)
         if content["pagination"]["total"] == 0:
             return False
         return True

mp_api/client/routes/materials/__init__.py

@@ -6,7 +6,7 @@
 from .dielectric import DielectricRester
 from .doi import DOIRester
 from .elasticity import ElasticityRester
-from .electrodes import ElectrodeRester
+from .electrodes import ConversionElectrodeRester, ElectrodeRester
 from .electronic_structure import (
     BandStructureRester,
     DosRester,

mp_api/client/routes/materials/electrodes.py

@@ -1,18 +1,18 @@
 from __future__ import annotations
 
+import warnings
 from collections import defaultdict
 
-from emmet.core.electrode import InsertionElectrodeDoc
+from emmet.core.electrode import ConversionElectrodeDoc, InsertionElectrodeDoc
 from pymatgen.core.periodic_table import Element
 
 from mp_api.client.core import BaseRester
 from mp_api.client.core.utils import validate_ids
 
 
-class ElectrodeRester(BaseRester[InsertionElectrodeDoc]):
-    suffix = "materials/insertion_electrodes"
-    document_model = InsertionElectrodeDoc  # type: ignore
+class BaseElectrodeRester(BaseRester):
     primary_key = "battery_id"
+    _exclude_search_fields: list[str] | None = None
 
     def search(  # pragma: ignore
         self,
@@ -38,7 +38,7 @@ def search(  # pragma: ignore
         chunk_size: int = 1000,
         all_fields: bool = True,
         fields: list[str] | None = None,
-    ) -> list[InsertionElectrodeDoc] | list[dict]:
+    ) -> list[InsertionElectrodeDoc | ConversionElectrodeDoc] | list[dict]:
         """Query using a variety of search criteria.
 
         Arguments:
@@ -74,11 +74,11 @@ def search(  # pragma: ignore
             num_chunks (int): Maximum number of chunks of data to yield. None will yield all possible.
             chunk_size (int): Number of data entries per chunk.
             all_fields (bool): Whether to return all fields in the document. Defaults to True.
-            fields (List[str]): List of fields in InsertionElectrodeDoc to return data for.
+            fields (List[str]): List of fields in InsertionElectrodeDoc or ConversionElectrodeDoc to return data for.
                 Default is battery_id and last_updated if all_fields is False.
 
         Returns:
-            ([InsertionElectrodeDoc], [dict]) List of insertion electrode documents or dictionaries.
+            ([InsertionElectrodeDoc or ConversionElectrodeDoc], [dict]) List of insertion/conversion electrode documents or dictionaries.
         """
         query_params = defaultdict(dict)  # type: dict
 
@@ -134,10 +134,43 @@ def search(  # pragma: ignore
                 else:
                     query_params.update({param: value})
 
+        excluded_fields = self._exclude_search_fields or []
+        ignored_fields = {
+            entry
+            for entry in excluded_fields
+            if query_params.pop(entry, None) is not None
+        }
+        if ignored_fields:
+            warnings.warn(
+                f"Ignoring fields {', '.join(ignored_fields)} which are not valid options for {self.__class__.__name__}"
+            )
+
         query_params = {
             entry: query_params[entry]
             for entry in query_params
             if query_params[entry] is not None
         }
 
         return super()._search(**query_params)
+
+
+class ElectrodeRester(BaseElectrodeRester):
+    """Search insertion electrode documents."""
+
+    suffix = "materials/insertion_electrodes"
+    document_model = InsertionElectrodeDoc  # type: ignore
+
+
+class ConversionElectrodeRester(BaseElectrodeRester):
+    """Search conversion electrode documents."""
+
+    suffix = "materials/conversion_electrodes"
+    document_model = ConversionElectrodeDoc  # type: ignore
+    # TODO: formula, chemsys, and elements do not appear to work in the API
+    _exclude_search_fields = [
+        "formula",
+        "chemsys",
+        "elements",
+        "stability_charge",
+        "stability_discharge",
+    ]

mp_api/client/routes/materials/electronic_structure.py

@@ -1,6 +1,5 @@
 from __future__ import annotations
 
-import json
 import warnings
 from collections import defaultdict
 
@@ -9,7 +8,6 @@
     DOSProjectionType,
     ElectronicStructureDoc,
 )
-from monty.json import MontyDecoder
 from pymatgen.analysis.magnetism.analyzer import Ordering
 from pymatgen.core.periodic_table import Element
 from pymatgen.electronic_structure.core import OrbitalType, Spin
@@ -234,11 +232,9 @@ def get_bandstructure_from_task_id(self, task_id: str):
         Returns:
             bandstructure (BandStructure): BandStructure or BandStructureSymmLine object
         """
-        decoder = MontyDecoder().decode if self.monty_decode else json.loads
         result = self._query_open_data(
             bucket="materialsproject-parsed",
             key=f"bandstructures/{task_id}.json.gz",
-            decoder=decoder,
         )[0]
 
         if result:
@@ -430,11 +426,9 @@ def get_dos_from_task_id(self, task_id: str):
         Returns:
             bandstructure (CompleteDos): CompleteDos object
         """
-        decoder = MontyDecoder().decode if self.monty_decode else json.loads
         result = self._query_open_data(
             bucket="materialsproject-parsed",
             key=f"dos/{task_id}.json.gz",
-            decoder=decoder,
         )[0]
 
         if result:

mp_api/client/routes/materials/materials.py

@@ -13,6 +13,7 @@
     BandStructureRester,
     BondsRester,
     ChemenvRester,
+    ConversionElectrodeRester,
     DielectricRester,
     DosRester,
     ElasticityRester,
@@ -62,6 +63,7 @@ class MaterialsRester(BaseRester[MaterialsDoc]):
         "robocrys",
         "synthesis",
         "insertion_electrodes",
+        "conversion_electrodes",
         "electronic_structure",
         "electronic_structure_bandstructure",
         "electronic_structure_dos",
@@ -92,6 +94,7 @@ class MaterialsRester(BaseRester[MaterialsDoc]):
     robocrys: RobocrysRester
     synthesis: SynthesisRester
     insertion_electrodes: ElectrodeRester
+    conversion_electrodes: ConversionElectrodeRester
     electronic_structure: ElectronicStructureRester
     electronic_structure_bandstructure: BandStructureRester
     electronic_structure_dos: DosRester