General upgrades (#390)

* Formula to criteria wildcard bug fix

* Add formula to criteria test

* Add exclude elements to mprester

* Increase default rate limit setting

* Default deprecation query to false and update epts

* Remove wulff endpoint

* Remove wulff import

* Fix potcar deserialization in task doc

* Bug and test fixes

* Temp xfails included

app.py

@@ -34,7 +34,6 @@
 surface_props_store_json = os.environ.get(
     "SURFACE_PROPS_STORE", "surface_props_store.json"
 )
-wulff_store_json = os.environ.get("WULFF_STORE", "wulff_store.json")
 robocrys_store_json = os.environ.get("ROBOCRYS_STORE", "robocrys_store.json")
 synth_store_json = os.environ.get("SYNTH_STORE", "synth_store.json")
 insertion_electrodes_store_json = os.environ.get(
@@ -181,13 +180,6 @@
         collection_name="surface_properties",
     )
 
-    wulff_store = MongoURIStore(
-        uri=f"mongodb+srv://{db_uri}",
-        database="mp_core",
-        key="task_id",
-        collection_name="wulff",
-    )
-
     robo_store = MongoURIStore(
         uri=f"mongodb+srv://{db_uri}",
         database="mp_core",
@@ -322,14 +314,13 @@
     doi_store = loadfn(doi_store_json)
     substrates_store = loadfn(substrates_store_json)
     surface_props_store = loadfn(surface_props_store_json)
-    wulff_store = loadfn(wulff_store_json)
     robo_store = loadfn(robocrys_store_json)
     synth_store = loadfn(synth_store_json)
     insertion_electrodes_store = loadfn(insertion_electrodes_store_json)
     molecules_store = loadfn(molecules_store_json)
     oxi_states_store = loadfn(oxi_states_store_json)
     provenance_store = loadfn(provenance_store_json)
-    ssummary_store = loadfn(summary_store_json)
+    summary_store = loadfn(summary_store_json)
 
     es_store = loadfn(es_store_json)
 
@@ -450,10 +441,6 @@
 
 resources.update({"surface_properties": [surface_props_resource(surface_props_store)]})
 
-# Wulff
-from mp_api.routes.wulff.resources import wulff_resource
-
-resources.update({"wulff": [wulff_resource(wulff_store)]})
 
 # Robocrystallographer
 from mp_api.routes.robocrys.resources import robo_resource, robo_search_resource

src/mp_api/core/settings.py

@@ -23,7 +23,7 @@ class MAPISettings(BaseSettings):
     db_version: str = Field("2021_prerelease", description="Database version")
 
     requests_per_min: int = Field(
-        60, description="Number of requests per minute to for rate limit."
+        100, description="Number of requests per minute to for rate limit."
     )
 
     class Config:

src/mp_api/matproj.py

@@ -470,6 +470,7 @@ def query(
         self,
         material_ids: Optional[List[MPID]] = None,
         chemsys_formula: Optional[str] = None,
+        exclude_elements: Optional[List[str]] = None,
         nsites: Optional[Tuple[int, int]] = None,
         volume: Optional[Tuple[float, float]] = None,
         density: Optional[Tuple[float, float]] = None,
@@ -530,6 +531,7 @@ def query(
             chemsys_formula (str): A chemical system (e.g., Li-Fe-O),
                 or formula including anonomyzed formula
                 or wild cards (e.g., Fe2O3, ABO3, Si*).
+            exclude_elements (List(str)): List of elements to exclude.
             crystal_system (CrystalSystem): Crystal system of material.
             spacegroup_number (int): Space group number of material.
             spacegroup_symbol (str): Space group symbol of the material in international short symbol notation.
@@ -599,6 +601,7 @@ def query(
         return self.summary.search_summary_docs(  # type: ignore
             material_ids=material_ids,
             chemsys_formula=chemsys_formula,
+            exclude_elements=exclude_elements,
             nsites=nsites,
             volume=volume,
             density=density,

src/mp_api/routes/__init__.py

@@ -7,7 +7,6 @@
 from mp_api.routes.grain_boundary.client import GrainBoundaryRester
 from mp_api.routes.substrates.client import SubstratesRester
 from mp_api.routes.surface_properties.client import SurfacePropertiesRester
-from mp_api.routes.wulff.client import WulffRester
 from mp_api.routes.phonon.client import PhononRester
 from mp_api.routes.elasticity.client import ElasticityRester
 from mp_api.routes.thermo.client import ThermoRester

src/mp_api/routes/electronic_structure/resources.py

@@ -6,6 +6,7 @@
 from mp_api.routes.materials.query_operators import (
     ElementsQuery,
     FormulaQuery,
+    DeprecationQuery,
 )
 
 from mp_api.routes.electronic_structure.query_operators import (
@@ -26,6 +27,7 @@ def es_resource(es_store):
             FormulaQuery(),
             ElementsQuery(),
             NumericQuery(model=ElectronicStructureDoc),
+            DeprecationQuery(),
             SortQuery(),
             PaginationQuery(),
             SparseFieldsQuery(
@@ -45,6 +47,7 @@ def bs_resource(es_store):
         ElectronicStructureDoc,
         query_operators=[
             BSDataQuery(),
+            DeprecationQuery(),
             SortQuery(),
             PaginationQuery(),
             SparseFieldsQuery(
@@ -84,6 +87,7 @@ def dos_resource(es_store):
         ElectronicStructureDoc,
         query_operators=[
             DOSDataQuery(),
+            DeprecationQuery(),
             SortQuery(),
             PaginationQuery(),
             SparseFieldsQuery(

src/mp_api/routes/materials/query_operators.py

@@ -82,7 +82,7 @@ class DeprecationQuery(QueryOperator):
     def query(
         self,
         deprecated: Optional[bool] = Query(
-            None, description="Whether the material is marked as deprecated",
+            False, description="Whether the material is marked as deprecated",
         ),
     ) -> STORE_PARAMS:
 

src/mp_api/routes/materials/utils.py

@@ -22,6 +22,10 @@ def formula_to_criteria(formula: str) -> Dict:
         if "*" in eles:
             crit["nelements"] = len(eles)
             crit["elements"] = {"$all": [ele for ele in eles if ele != "*"]}
+
+            if crit["elements"]["$all"] == []:
+                del crit["elements"]
+
             return crit
         else:
             chemsys = "-".join(sorted(eles))
@@ -34,17 +38,11 @@ def formula_to_criteria(formula: str) -> Dict:
 
         formula_dummies = formula.replace("*", "{}").format(*dummies[:nstars])
 
-        integer_formula = Composition(formula_dummies).get_integer_formula_and_factor()[
-            0
-        ]
+        integer_formula = Composition(formula_dummies).get_integer_formula_and_factor()[0]
         comp = Composition(integer_formula).reduced_composition
         crit = dict()
         crit["formula_anonymous"] = comp.anonymized_formula
-        real_elts = [
-            str(e)
-            for e in comp.elements
-            if not e.as_dict().get("element", "A") in dummies
-        ]
+        real_elts = [str(e) for e in comp.elements if not e.as_dict().get("element", "A") in dummies]
 
         for el, n in comp.to_reduced_dict.items():
             if el in real_elts:

src/mp_api/routes/provenance/resources.py

@@ -1,5 +1,6 @@
 from maggma.api.resource import ReadOnlyResource
 from maggma.api.query_operator import PaginationQuery
+from mp_api.routes.materials.query_operators import DeprecationQuery
 
 from emmet.core.provenance import ProvenanceDoc
 
@@ -8,7 +9,7 @@ def provenance_resource(provenance_store):
     resource = ReadOnlyResource(
         provenance_store,
         ProvenanceDoc,
-        query_operators=[PaginationQuery()],
+        query_operators=[DeprecationQuery(), PaginationQuery()],
         tags=["Provenance"],
         disable_validation=True,
         enable_default_search=False,

src/mp_api/routes/summary/client.py

@@ -18,6 +18,7 @@ def search_summary_docs(
         self,
         material_ids: Optional[List[MPID]] = None,
         chemsys_formula: Optional[str] = None,
+        exclude_elements: Optional[List[str]] = None,
         nsites: Optional[Tuple[int, int]] = None,
         volume: Optional[Tuple[float, float]] = None,
         density: Optional[Tuple[float, float]] = None,
@@ -78,6 +79,7 @@ def search_summary_docs(
             chemsys_formula (str): A chemical system (e.g., Li-Fe-O),
                 or formula including anonomyzed formula
                 or wild cards (e.g., Fe2O3, ABO3, Si*).
+            exclude_elements (List(str)): List of elements to exclude.
             crystal_system (CrystalSystem): Crystal system of material.
             spacegroup_number (int): Space group number of material.
             spacegroup_symbol (str): Space group symbol of the material in international short symbol notation.
@@ -199,6 +201,9 @@ def search_summary_docs(
         if chemsys_formula:
             query_params.update({"formula": chemsys_formula})
 
+        if exclude_elements is not None:
+            query_params.update({"exclude_elements": ",".join(exclude_elements)})
+
         query_params.update(
             {
                 "crystal_system": crystal_system,

src/mp_api/routes/tasks/models.py

@@ -1,14 +1,15 @@
 from datetime import datetime
 from enum import Enum
-from typing import List
+from json import decoder
+from typing import List, Dict
 
 from monty.json import MontyDecoder
 from pydantic import BaseModel, Field, validator
 
 from pymatgen.core.structure import Structure
 from pymatgen.core.composition import Composition
 from pymatgen.core.periodic_table import Element
-from pymatgen.io.vasp import Incar, Poscar, Kpoints, Potcar
+from pymatgen.io.vasp import Incar, Poscar, Kpoints
 from pymatgen.core.trajectory import Trajectory
 
 monty_decoder = MontyDecoder()
@@ -30,6 +31,14 @@ class TaskType(str, Enum):
     GGA_U_Structure_Optimization = "GGA+U Structure Optimization"
 
 
+class Potcar(BaseModel):
+    functional: str = Field(None, description="Functional type use in the calculation.")
+
+    symbols: List[str] = Field(
+        None, description="List of VASP potcar symbols used in the calculation."
+    )
+
+
 class OrigInputs(BaseModel):
     incar: Incar = Field(
         None, description="Pymatgen object representing the INCAR file",

tests/materials/test_utils.py

@@ -19,3 +19,4 @@ def test_formula_to_criteria():
     # Chemsys
     assert formula_to_criteria("Si-O") == {"chemsys": "O-Si"}
     assert formula_to_criteria("Si-*") == {"elements": {"$all": ["Si"]}, "nelements": 2}
+    assert formula_to_criteria("*-*-*") == {"nelements": 3}