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Dielectric, Piezoelectric, Magnetism, Bonds, and Phase Diagrams (#420)
* Emmet bump * Update dielectric, piezoelectric, magnetism * task_id to material_id in clients * Fix collection names * Remove sub doc fields from client tests * Ignore some endpoints in tests temp * Temp xfail on endpoints * Bump emmet * Add bonds endpoint * Bump emmet * Phase diagram endpoint added to thermo * Temp xfail on thermo pd client method * Linting * Alter materials and thermo collection names * Fix tests * Linting * Fix robocrys test * Update robocrys test * Update database names * Fix missing fstrings * Remove stray print * Temp xfail on find structure test
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Jason Munro
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Nov 10, 2021
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,105 @@ | ||
| from typing import List, Optional, Tuple | ||
| from collections import defaultdict | ||
|
|
||
| from mp_api.core.client import BaseRester | ||
| from emmet.core.bonds import BondingDoc | ||
|
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| class BondsRester(BaseRester[BondingDoc]): | ||
|
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| suffix = "bonds" | ||
| document_model = BondingDoc # type: ignore | ||
| primary_key = "material_id" | ||
|
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| def search_bonds_docs( | ||
| self, | ||
| max_bond_length: Optional[Tuple[float, float]] = None, | ||
| min_bond_length: Optional[Tuple[float, float]] = None, | ||
| mean_bond_length: Optional[Tuple[float, float]] = None, | ||
| coordination_envs: Optional[List[str]] = None, | ||
| coordination_envs_anonymous: Optional[List[str]] = None, | ||
| sort_field: Optional[str] = None, | ||
| ascending: Optional[bool] = None, | ||
| num_chunks: Optional[int] = None, | ||
| chunk_size: int = 1000, | ||
| all_fields: bool = True, | ||
| fields: Optional[List[str]] = None, | ||
| ): | ||
| """ | ||
| Query dielectric docs using a variety of search criteria. | ||
| Arguments: | ||
| max_bond_length (Tuple[float,float]): Minimum and maximum value for the maximum bond length | ||
| in the structure to consider. | ||
| min_bond_length (Tuple[float,float]): Minimum and maximum value for the minimum bond length | ||
| in the structure to consider. | ||
| mean_bond_length (Tuple[float,float]): Minimum and maximum value for the mean bond length | ||
| in the structure to consider. | ||
| coordination_envs (List[str]): List of coordination environments to consider (e.g. ['Mo-S(6)', 'S-Mo(3)']). | ||
| coordination_envs_anonymous (List[str]): List of anonymous coordination environments to consider | ||
| (e.g. ['A-B(6)', 'A-B(3)']). | ||
| sort_field (str): Field used to sort results. | ||
| ascending (bool): Whether sorting should be in ascending order. | ||
| 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 DielectricDoc to return data for. | ||
| Default is material_id and last_updated if all_fields is False. | ||
| Returns: | ||
| ([BondingDoc]) List of bonding documents. | ||
| """ | ||
|
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| query_params = defaultdict(dict) # type: dict | ||
|
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| if max_bond_length: | ||
| query_params.update( | ||
| { | ||
| "max_bond_length_min": max_bond_length[0], | ||
| "max_bond_length_max": max_bond_length[1], | ||
| } | ||
| ) | ||
|
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| if min_bond_length: | ||
| query_params.update( | ||
| { | ||
| "min_bond_length_min": min_bond_length[0], | ||
| "min_bond_length_max": min_bond_length[1], | ||
| } | ||
| ) | ||
|
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| if mean_bond_length: | ||
| query_params.update( | ||
| { | ||
| "mean_bond_length_min": mean_bond_length[0], | ||
| "mean_bond_length_max": mean_bond_length[1], | ||
| } | ||
| ) | ||
|
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| if coordination_envs is not None: | ||
| query_params.update({"coordination_envs": ",".join(coordination_envs)}) | ||
|
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| if coordination_envs_anonymous is not None: | ||
| query_params.update( | ||
| {"coordination_envs_anonymous": ",".join(coordination_envs_anonymous)} | ||
| ) | ||
|
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| if sort_field: | ||
| query_params.update({"sort_field": sort_field}) | ||
|
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| if ascending is not None: | ||
| query_params.update({"ascending": ascending}) | ||
|
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| query_params = { | ||
| entry: query_params[entry] | ||
| for entry in query_params | ||
| if query_params[entry] is not None | ||
| } | ||
|
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| return super().search( | ||
| num_chunks=num_chunks, | ||
| chunk_size=chunk_size, | ||
| all_fields=all_fields, | ||
| fields=fields, | ||
| **query_params | ||
| ) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,102 @@ | ||
| from typing import Optional | ||
| from fastapi import Query | ||
| from maggma.api.query_operator import QueryOperator | ||
| from maggma.api.utils import STORE_PARAMS | ||
|
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| from collections import defaultdict | ||
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| class BondLengthQuery(QueryOperator): | ||
| """ | ||
| Method to generate a query on bond length data. | ||
| """ | ||
|
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| def query( | ||
| self, | ||
| max_bond_length_max: Optional[float] = Query( | ||
| None, | ||
| description="Maximum value for the maximum bond length in the structure.", | ||
| ), | ||
| max_bond_length_min: Optional[float] = Query( | ||
| None, | ||
| description="Minimum value for the maximum bond length in the structure.", | ||
| ), | ||
| min_bond_length_max: Optional[float] = Query( | ||
| None, | ||
| description="Maximum value for the minimum bond length in the structure.", | ||
| ), | ||
| min_bond_length_min: Optional[float] = Query( | ||
| None, | ||
| description="Minimum value for the minimum bond length in the structure.", | ||
| ), | ||
| mean_bond_length_max: Optional[float] = Query( | ||
| None, | ||
| description="Maximum value for the mean bond length in the structure.", | ||
| ), | ||
| mean_bond_length_min: Optional[float] = Query( | ||
| None, | ||
| description="Minimum value for the mean bond length in the structure.", | ||
| ), | ||
| ) -> STORE_PARAMS: | ||
|
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| crit = defaultdict(dict) # type: dict | ||
|
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| d = { | ||
| "bond_length_stats.max": [max_bond_length_min, max_bond_length_max], | ||
| "bond_length_stats.min": [min_bond_length_min, min_bond_length_max], | ||
| "bond_length_stats.mean": [mean_bond_length_min, mean_bond_length_max], | ||
| } | ||
|
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| for entry in d: | ||
| if d[entry][0] is not None: | ||
| crit[entry]["$gte"] = d[entry][0] | ||
|
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| if d[entry][1] is not None: | ||
| crit[entry]["$lte"] = d[entry][1] | ||
|
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| return {"criteria": crit} | ||
|
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| def ensure_indexes(self): # pragma: no cover | ||
| keys = [ | ||
| "bond_length_stats.max", | ||
| "bond_length_stats.min", | ||
| "bond_length_stats.mean", | ||
| ] | ||
| return [(key, False) for key in keys] | ||
|
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|
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| class CoordinationEnvsQuery(QueryOperator): | ||
| """ | ||
| Method to generate a query on coordination environment data. | ||
| """ | ||
|
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| def query( | ||
| self, | ||
| coordination_envs: Optional[str] = Query( | ||
| None, | ||
| description="Query by coordination environments in the material composition as a comma-separated list\ | ||
| (e.g. 'Mo-S(6),S-Mo(3)')", | ||
| ), | ||
| coordination_envs_anonymous: Optional[str] = Query( | ||
| None, | ||
| description="Query by anonymous coordination environments in the material composition as a comma-separated\ | ||
| list (e.g. 'A-B(6),A-B(3)')", | ||
| ), | ||
| ) -> STORE_PARAMS: | ||
|
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| crit = {} # type: dict | ||
|
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| if coordination_envs: | ||
| env_list = [env.strip() for env in coordination_envs.split(",")] | ||
| crit["coordination_envs"] = {"$all": [str(env) for env in env_list]} | ||
|
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| if coordination_envs_anonymous: | ||
| env_list = [env.strip() for env in coordination_envs_anonymous.split(",")] | ||
| crit["coordination_envs_anonymous"] = { | ||
| "$all": [str(env) for env in env_list] | ||
| } | ||
|
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| return {"criteria": crit} | ||
|
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| def ensure_indexes(self): # pragma: no cover | ||
| return [("coordination_envs", False), ("coordination_envs_anonymous", False)] |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,26 @@ | ||
| from maggma.api.resource import ReadOnlyResource | ||
| from emmet.core.bonds import BondingDoc | ||
|
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| from maggma.api.query_operator import PaginationQuery, SortQuery, SparseFieldsQuery | ||
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| from mp_api.routes.bonds.query_operators import BondLengthQuery, CoordinationEnvsQuery | ||
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| def bonds_resource(bonds_store): | ||
| resource = ReadOnlyResource( | ||
| bonds_store, | ||
| BondingDoc, | ||
| query_operators=[ | ||
| BondLengthQuery(), | ||
| CoordinationEnvsQuery(), | ||
| SortQuery(), | ||
| PaginationQuery(), | ||
| SparseFieldsQuery( | ||
| BondingDoc, default_fields=["material_id", "last_updated"], | ||
| ), | ||
| ], | ||
| tags=["Bonds"], | ||
| disable_validation=True, | ||
| ) | ||
|
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| return resource |
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