Update client to fully reconstruct pydantic models via use of native …

…pymatgen objects (#223) * Bump required monty version * Change how pydantic objects are reconstructed in the client * Add comment * Start switch to using native pymatgen models * Update tasks endpoint to use pymatgen models * Pymatgen version import fix * task_id list search added to tasks * Insertion electrode model and query op updates * Multiple task_id search added to molecules * Deprecation query changed to list of task_ids * Linting * client: catch __version__ import for old pymatgen * dependabot PRs Bump boto3 from 1.17.22 to 1.17.32 Bumps [boto3](https://github.com/boto/boto3) from 1.17.22 to 1.17.32. - [Release notes](https://github.com/boto/boto3/releases) - [Changelog](https://github.com/boto/boto3/blob/develop/CHANGELOG.rst) - [Commits](boto/boto3@1.17.22...1.17.32) Signed-off-by: dependabot[bot] <support@github.com> Bump flake8 from 3.8.4 to 3.9.0 Bumps [flake8](https://gitlab.com/pycqa/flake8) from 3.8.4 to 3.9.0. - [Release notes](https://gitlab.com/pycqa/flake8/tags) - [Commits](https://gitlab.com/pycqa/flake8/compare/3.8.4...3.9.0) Signed-off-by: dependabot[bot] <support@github.com> Bump pre-commit from 2.11.0 to 2.11.1 Bumps [pre-commit](https://github.com/pre-commit/pre-commit) from 2.11.0 to 2.11.1. - [Release notes](https://github.com/pre-commit/pre-commit/releases) - [Changelog](https://github.com/pre-commit/pre-commit/blob/master/CHANGELOG.md) - [Commits](pre-commit/pre-commit@v2.11.0...v2.11.1) Signed-off-by: dependabot[bot] <support@github.com> Bump pycodestyle from 2.6.0 to 2.7.0 Bumps [pycodestyle](https://github.com/PyCQA/pycodestyle) from 2.6.0 to 2.7.0. - [Release notes](https://github.com/PyCQA/pycodestyle/releases) - [Changelog](https://github.com/PyCQA/pycodestyle/blob/master/CHANGES.txt) - [Commits](https://github.com/PyCQA/pycodestyle/commits) Signed-off-by: dependabot[bot] <support@github.com> * Bump boto3 from 1.17.32 to 1.17.33 Bumps [boto3](https://github.com/boto/boto3) from 1.17.32 to 1.17.33. - [Release notes](https://github.com/boto/boto3/releases) - [Changelog](https://github.com/boto/boto3/blob/develop/CHANGELOG.rst) - [Commits](boto/boto3@1.17.32...1.17.33) Signed-off-by: dependabot[bot] <support@github.com> * Wildcard added to chemsys search * InsertionElectrode object added to model * API pinned to temp monty fix * Linting * github testing updated from master to main * Mypy fixes * Ignore missing imports mypy * Literal pulled from typing_extensions * More linting * added more fields to electrode doc (#229) * added more fields to electrode doc * added elements field * linting * update * more useful fields Co-authored-by: Jason Munro <jmunro@lbl.gov> Co-authored-by: Patrick Huck <phuck@lbl.gov> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: JSX <jmmshn@gmail.com>
materialsproject · Mar 24, 2021 · a21a96f · a21a96f
1 parent 5216ab0
commit a21a96f
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Showing 24 changed files with 252 additions and 207 deletions.
diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
@@ -3,11 +3,11 @@ name: testing
 on:
   push:
     branches:
-      - master
+      - main
 
   pull_request:
     branches:
-      - master
+      - main
 
 jobs:
   lint:

diff --git a/requirements-server.txt b/requirements-server.txt
@@ -3,4 +3,4 @@ maggma==0.26.0
 uvicorn==0.13.4
 gunicorn[gevent]>=20.0.1
 aws-xray-sdk==2.6.0
-boto3==1.17.22
+boto3==1.17.33
diff --git a/requirements-testing.txt b/requirements-testing.txt
@@ -1,9 +1,9 @@
-pre-commit==2.11.0
+pre-commit==2.11.1
 pytest==6.2.2
 pytest-asyncio==0.14.0
 pytest-cov==2.11.1
 pytest-mock==3.5.1
-pycodestyle==2.6.0
-flake8==3.8.4
+pycodestyle==2.7.0
+flake8==3.9.0
 mypy==0.812
 mypy-extensions==0.4.3
diff --git a/requirements.txt b/requirements.txt
@@ -3,3 +3,5 @@ pymatgen>=2020.9.14,<2022
 typing-extensions==3.7.4.3
 maggma==0.26.0
 requests==2.25.1
+git+git://github.com/mkhorton/monty@patch-4#egg=monty
+#monty>=2021.3.3
diff --git a/setup.cfg b/setup.cfg
@@ -16,19 +16,5 @@ max-line-length = 120
 [pydocstyle]
 ignore = D105,D2,D4
 
-[mypy-pymatgen.*]
-ignore_missing_imports = True
-
-
-[mypy-pytest]
-ignore_missing_imports = True
-
-
-[mypy-uvicorn]
-ignore_missing_imports = True
-
-[mypy-monty.*]
-ignore_missing_imports = True
-
-[mypy-aws_xray_sdk.*]
+[mypy]
 ignore_missing_imports = True
diff --git a/src/mp_api/charge_density/client.py b/src/mp_api/charge_density/client.py
@@ -38,12 +38,12 @@ def get_calculation_details(self, material_id: str):
         """
 
         base_endpoint = "/".join(self.endpoint.split("/")[0:3])
-        task_rester = TaskRester(api_key=self.api_key, endpoint=base_endpoint)
+        task_rester = TaskRester(api_key=self.api_key, endpoint=base_endpoint)  # type: ignore
 
-        result = task_rester.get_task_from_material_id(
+        result = task_rester.get_task_from_material_id(  # type: ignore
             material_id, fields=["task_id", "orig_inputs"]
         ).get("data")[0]
 
-        task_rester.session.close()
+        task_rester.session.close()  # type: ignore
 
         return result
diff --git a/src/mp_api/core/api.py b/src/mp_api/core/api.py
@@ -6,7 +6,7 @@
 from datetime import datetime
 from monty.json import MSONable
 from mp_api.core.resource import Resource
-from pymatgen import __version__ as pmg_version  # type: ignore
+from pymatgen.core import __version__ as pmg_version  # type: ignore
 from fastapi.openapi.utils import get_openapi
 
 

diff --git a/src/mp_api/core/client.py b/src/mp_api/core/client.py
@@ -16,10 +16,15 @@
 
 import requests
 from monty.json import MontyDecoder
-from pymatgen import __version__ as pmg_version  # type: ignore
 from requests.exceptions import RequestException
 from pydantic import BaseModel
 
+try:
+    from pymatgen.core import __version__ as pmg_version  # type: ignore
+except ImportError:
+    # fallback to root-level import for older pymatgen versions
+    from pymatgen import __version__ as pmg_version  # type: ignore
+
 # TODO: think about how to migrate from PMG_MAPI_KEY
 DEFAULT_API_KEY = environ.get("MP_API_KEY", None)
 DEFAULT_ENDPOINT = environ.get("MP_API_ENDPOINT", "https://api.materialsproject.org/")
@@ -199,7 +204,7 @@ def _query_resource(
                     data = json.loads(response.text)
 
                 if self.document_model:
-                    data["data"] = [self.document_model.construct(**d) for d in data["data"]]  # type: ignore
+                    data["data"] = [self.document_model.parse_obj(d) for d in data["data"]]  # type: ignore
 
                 return data
 

diff --git a/src/mp_api/electrodes/models.py b/src/mp_api/electrodes/models.py
@@ -1,11 +1,14 @@
 from monty.json import MontyDecoder
 from pymatgen.core.periodic_table import Element
-from typing import Dict, List
+from pymatgen.core import Structure
+from typing import Dict, List, Union
 from datetime import datetime
 
 from pydantic import BaseModel, Field, validator
 from mp_api.materials.models import Composition
 
+from pymatgen.apps.battery.insertion_battery import InsertionElectrode
+
 
 class VoltageStep(BaseModel):
     """
@@ -21,13 +24,11 @@ class VoltageStep(BaseModel):
     )
 
     average_voltage: float = Field(
-        None,
-        description="The average voltage in V for a particular voltage step.",
+        None, description="The average voltage in V for a particular voltage step.",
     )
 
     min_voltage: float = Field(
-        None,
-        description="The min voltage in V for a particular voltage step.",
+        None, description="The min voltage in V for a particular voltage step.",
     )
 
     capacity_grav: float = Field(None, description="Gravimetric capacity in mAh/g.")
@@ -55,6 +56,14 @@ class InsertionVoltageStep(VoltageStep):
     Features specific to insertion electrode
     """
 
+    formula_charge: str = Field(
+        None, description="The chemical formula of the charged material."
+    )
+
+    formula_discharge: str = Field(
+        None, description="The chemical formula of the discharged material."
+    )
+
     stability_charge: float = Field(
         None, description="The energy above hull of the charged material."
     )
@@ -63,17 +72,29 @@ class InsertionVoltageStep(VoltageStep):
         None, description="The energy above hull of the discharged material."
     )
 
+    id_charge: Union[str] = Field(
+        None, description="The material-id of the charged structure."
+    )
+
+    id_discharge: Union[str] = Field(
+        None, description="The material-id of the discharged structure."
+    )
+
 
 class InsertionElectrodeDoc(InsertionVoltageStep):
 
     battery_id: str = Field(None, description="The id for this battery document.")
 
-    framework: Composition = Field(
+    framework_formula: str = Field(
+        None, description="The id for this battery document."
+    )
+
+    host_structure: Structure = Field(
         None,
-        description="The composition of the host framework (structure without the working ion)",
+        description="Host structure (structure without the working ion)",
     )
 
-    voltage_pairs: List[InsertionVoltageStep] = Field(
+    adj_pairs: List[InsertionVoltageStep] = Field(
         None,
         description="Returns all the Voltage Steps",
     )
@@ -86,7 +107,7 @@ class InsertionElectrodeDoc(InsertionVoltageStep):
     num_steps: float = Field(
         None,
         description="The number of distinct voltage steps in from fully charge to "
-        "discharge based on the stable intermediate states",
+                    "discharge based on the stable intermediate states",
     )
 
     max_voltage_step: float = Field(
@@ -98,6 +119,32 @@ class InsertionElectrodeDoc(InsertionVoltageStep):
         description="Timestamp for the most recent calculation for this Material document",
     )
 
+    framework: Composition = Field(
+        None,
+        description="The chemical compositions of the host framework",
+    )
+
+    material_ids: List[str] = Field(
+        None,
+        description="The ids of all structures that matched to the present host lattice, regardless of stability. "
+                    "The stable entries can be found in the adjacent pairs.",
+    )
+
+    elements: List[Element] = Field(
+        None,
+        description="The atomic species contained in this electrode.",
+    )
+
+    chemsys: str = Field(
+        None,
+        description="The chemical system this electrode belongs to. "
+                    "Note: The conversion electrode can be calculated on this chemical system",
+    )
+
+    electrode_object: InsertionElectrode = Field(
+        None, description="Returns InsertionElectrode object",
+    )
+
     # Make sure that the datetime field is properly formatted
     @validator("last_updated", pre=True)
     def last_updated_dict_ok(cls, v):
@@ -118,14 +165,12 @@ class ConversionElectrode(ConversionVoltageStep):
 
     battery_id: str = Field(None, description="The id for this battery document.")
 
-    voltage_pairs: List[ConversionVoltageStep] = Field(
-        None,
-        description="Returns all the Voltage Steps",
+    electrode_object: InsertionElectrode = Field(
+        None, description="Returns InsertionElectrode object",
     )
 
     working_ion: str = Field(
-        None,
-        description="The working ion as an Element object",
+        None, description="The working ion as an Element object",
     )
 
     num_steps: float = Field(

diff --git a/src/mp_api/electrodes/query_operators.py b/src/mp_api/electrodes/query_operators.py
@@ -46,20 +46,16 @@ def query(
             description="Minimum value for the minimum voltage for a particular voltage step in V.",
         ),
         capacity_grav_max: Optional[float] = Query(
-            None,
-            description="Maximum value for the gravimetric capacity in maH/g.",
+            None, description="Maximum value for the gravimetric capacity in maH/g.",
         ),
         capacity_grav_min: Optional[float] = Query(
-            None,
-            description="Minimum value for the gravimetric capacity in maH/g.",
+            None, description="Minimum value for the gravimetric capacity in maH/g.",
         ),
         capacity_vol_max: Optional[float] = Query(
-            None,
-            description="Maximum value for the volumetric capacity in maH/cc.",
+            None, description="Maximum value for the volumetric capacity in maH/cc.",
         ),
         capacity_vol_min: Optional[float] = Query(
-            None,
-            description="Minimum value for the volumetric capacity in maH/cc.",
+            None, description="Minimum value for the volumetric capacity in maH/cc.",
         ),
         energy_grav_max: Optional[float] = Query(
             None,

diff --git a/src/mp_api/materials/models/doc.py b/src/mp_api/materials/models/doc.py
@@ -3,7 +3,9 @@
 from pydantic import BaseModel, Field, validator
 from pymatgen.core.periodic_table import Element
 from datetime import datetime
-from mp_api.materials.models import Structure, Composition, CrystalSystem
+from mp_api.materials.models import CrystalSystem
+from pymatgen.core.structure import Structure
+from pymatgen.core.composition import Composition
 
 
 class SymmetryData(BaseModel):

diff --git a/src/mp_api/materials/utils.py b/src/mp_api/materials/utils.py
@@ -15,7 +15,20 @@ def formula_to_criteria(formula: str) -> Dict:
     """
     dummies = "ADEGJLMQRXZ"
 
-    if "*" in formula:
+    if "-" in formula:
+        crit = {}  # type: dict
+        eles = formula.split("-")
+
+        if "*" in eles:
+            crit["nelements"] = len(eles)
+            crit["elements"] = {"$in": [ele for ele in eles if ele != "*"]}
+            return crit
+        else:
+            chemsys = "-".join(sorted(eles))
+            crit["chemsys"] = chemsys
+            return crit
+
+    elif "*" in formula:
         # Wild card in formula
         nstars = formula.count("*")
 
@@ -39,15 +52,6 @@ def formula_to_criteria(formula: str) -> Dict:
 
         return crit
 
-    elif "-" in formula:
-        crit = {}
-        eles = formula.split("-")
-        chemsys = "-".join(sorted(eles))
-
-        crit["chemsys"] = chemsys
-
-        return crit
-
     elif any(isinstance(el, DummySpecies) for el in Composition(formula)):
         # Assume fully anonymized formula
         return {"formula_anonymous": Composition(formula).anonymized_formula}

diff --git a/src/mp_api/molecules/resources.py b/src/mp_api/molecules/resources.py
@@ -7,7 +7,7 @@
     MoleculeElementsQuery,
     MoleculeFormulaQuery,
 )
-from mp_api.search.query_operators import SearchTaskIDsQuery
+from mp_api.tasks.query_operators import MultipleTaskIDsQuery
 
 
 def molecules_resource(molecules_store):
@@ -18,7 +18,7 @@ def molecules_resource(molecules_store):
             MoleculeBaseQuery(),
             MoleculeElementsQuery(),
             MoleculeFormulaQuery(),
-            SearchTaskIDsQuery(),
+            MultipleTaskIDsQuery(),
             SortQuery(),
             PaginationQuery(),
             SparseFieldsQuery(MoleculesDoc, default_fields=["task_id"]),