Endpoint updates (#326)

* Update phonon endpoint

* Fix tests and include explicit methods in mprester

* Linting

* Fix phonon client stubs

* Skip client tests if no API key found.

* Electrode client test xfail

* Add chemsys to materials util test

* Add wildcard to materials utils test

* Enable bare response on most endpoints

* Increase rate limit setting

* Lower request rate limit setting

app.py

@@ -27,7 +27,6 @@
 )
 magnetism_store_json = os.environ.get("MAGNETISM_STORE", "magnetism_store.json")
 phonon_bs_store_json = os.environ.get("PHONON_BS_STORE", "phonon_bs_store.json")
-phonon_img_store_json = os.environ.get("PHONON_IMG_STORE", "phonon_img_store.json")
 eos_store_json = os.environ.get("EOS_STORE", "eos_store.json")
 similarity_store_json = os.environ.get("SIMILARITY_STORE", "similarity_store.json")
 xas_store_json = os.environ.get("XAS_STORE", "xas_store.json")
@@ -118,15 +117,8 @@
     phonon_bs_store = MongoURIStore(
         uri=f"mongodb+srv://{db_uri}",
         database="mp_core",
-        key="task_id",
-        collection_name="phonon_bs",
-    )
-
-    phonon_img_store = MongoURIStore(
-        uri=f"mongodb+srv://{db_uri}",
-        database="mp_core",
-        key="task_id",
-        collection_name="phonon_img",
+        key="material_id",
+        collection_name="pmg_ph_bs",
     )
 
     eos_store = MongoURIStore(
@@ -317,7 +309,6 @@
     dielectric_piezo_store = loadfn(dielectric_piezo_store_json)
     magnetism_store = loadfn(magnetism_store_json)
     phonon_bs_store = loadfn(phonon_bs_store_json)
-    phonon_img_store = loadfn(phonon_img_store_json)
     eos_store = loadfn(eos_store_json)
     similarity_store = loadfn(similarity_store_json)
     xas_store = loadfn(xas_store_json)
@@ -405,16 +396,9 @@
 resources.update({"piezoelectric": [piezo_resource(dielectric_piezo_store)]})
 
 # Phonon
-from mp_api.routes.phonon.resources import phonon_bs_resource, phonon_img_resource
+from mp_api.routes.phonon.resources import phonon_bsdos_resource
 
-resources.update(
-    {
-        "phonon": [
-            phonon_img_resource(phonon_img_store),
-            phonon_bs_resource(phonon_bs_store),
-        ]
-    }
-)
+resources.update({"phonon": [phonon_bsdos_resource(phonon_bs_store),]})
 
 # EOS
 from mp_api.routes.eos.resources import eos_resource

src/mp_api/matproj.py

@@ -1,4 +1,4 @@
-from os import environ
+from os import environ, path
 import warnings
 from typing import Optional, Tuple, List
 from enum import Enum, unique
@@ -11,6 +11,7 @@
 from emmet.core.symmetry import CrystalSystem
 
 from mp_api.core.client import BaseRester
+from mp_api.routes.electronic_structure.models.core import BSPathType
 from mp_api.routes import *
 
 _DEPRECATION_WARNING = (
@@ -106,27 +107,18 @@ def __init__(
                 self, cls.suffix.replace("/", "_"), rester,
             )
 
-        self.find_structure = self.materials.find_structure
-
-        self.get_bandstructure_by_material_id = (
-            self.electronic_structure_bandstructure.get_bandstructure_from_material_id
-        )
-        self.get_dos_by_material_id = (
-            self.electronic_structure_dos.get_dos_from_material_id
-        )
-
         self.get_charge_density_from_calculation_id = (
             self.charge_density.get_charge_density_from_calculation_id
         )
 
-        self.get_charge_density_calculation_details = (
-            self.charge_density.get_charge_density_calculation_details
-        )
-
         self.get_charge_density_calculation_ids_from_material_id = (
             self.charge_density.get_charge_density_calculation_ids_from_material_id
         )
 
+        self.get_charge_density_calculation_details = (
+            self.charge_density.get_charge_density_calculation_details
+        )
+
     def __enter__(self):
         """
         Support for "with" context.
@@ -287,6 +279,32 @@ def get_structures(self, chemsys_formula, final=True):
 
             return structures
 
+    def find_structure(
+        self, filename_or_structure, ltol=0.2, stol=0.3, angle_tol=5, limit=1
+    ):
+        """
+        Finds matching structures on the Materials Project site.
+        Args:
+            filename_or_structure: filename or Structure object
+            ltol: fractional length tolerance
+            stol: site tolerance
+            angle_tol: angle tolerance in degrees
+            limit: amount of structure matches to limit to
+        Returns:
+            A list of matching materials project ids for structure, \
+                including normalized rms distances and max distances between paired sites.
+        Raises:
+            MPRestError
+        """
+
+        return self.materials.find_structure(
+            filename_or_structure,
+            ltol=ltol,
+            stol=stol,
+            angle_tol=angle_tol,
+            limit=limit,
+        )
+
     def get_entries(
         self, chemsys_formula, sort_by_e_above_hull=False,
     ):
@@ -343,6 +361,41 @@ def get_entry_by_material_id(self, material_id):
             ).entries.values()
         )
 
+    def get_bandstructure_by_material_id(
+        self,
+        material_id: str,
+        path_type: BSPathType = BSPathType.setyawan_curtarolo,
+        line_mode=True,
+    ):
+        """
+        Get the band structure pymatgen object associated with a Materials Project ID.
+
+        Arguments:
+            materials_id (str): Materials Project ID for a material
+            path_type (BSPathType): k-point path selection convention
+            line_mode (bool): Whether to return data for a line-mode calculation
+
+        Returns:
+            bandstructure (Union[BandStructure, BandStructureSymmLine]): BandStructure or BandStructureSymmLine object
+        """
+        return self.electronic_structure_bandstructure.get_bandstructure_from_material_id(  # type: ignore
+            material_id=material_id, path_type=path_type, line_mode=line_mode
+        )
+
+    def get_dos_by_material_id(self, material_id: str):
+        """
+        Get the complete density of states pymatgen object associated with a Materials Project ID.
+
+        Arguments:
+            materials_id (str): Materials Project ID for a material
+
+        Returns:
+            dos (CompleteDos): CompleteDos object
+        """
+        return self.electronic_structure_dos.get_dos_from_material_id(  # type: ignore
+            material_id=material_id
+        )
+
     def get_phonon_dos_by_material_id(self, material_id):
         """
         Get phonon density of states data corresponding to a material_id.
@@ -354,7 +407,7 @@ def get_phonon_dos_by_material_id(self, material_id):
              CompletePhononDos: A phonon DOS object.
 
         """
-        raise NotImplementedError
+        return self.phonon.get_document_by_id(material_id, fields=["ph_dos"]).ph_dos
 
     def get_phonon_bandstructure_by_material_id(self, material_id):
         """
@@ -366,9 +419,20 @@ def get_phonon_bandstructure_by_material_id(self, material_id):
         Returns:
             PhononBandStructureSymmLine:  phonon band structure.
         """
-        doc = self.phonon.get_document_by_id(material_id)
+        return self.phonon.get_document_by_id(material_id, fields=["ph_bs"]).ph_bs
 
-        return doc.ph_bs
+    def get_charge_density_by_material_id(self, material_id: str):
+        """
+        Get charge density data for a given Materials Project ID.
+
+        Arguments:
+            material_id (str): Material Project ID
+
+        Returns:
+            chgcar (dict): Pymatgen CHGCAR object.
+        """
+
+        return self.charge_density.get_charge_density_from_material_id(material_id)  # type: ignore
 
     def query(
         self,
@@ -559,39 +623,6 @@ def submit_structures(self, structures, public_name, public_email):
         # TODO: call new MPComplete endpoint
         raise NotImplementedError
 
-    def get_stability(self, entries):
-        """
-        Returns the stability of all entries.
-        """
-        # TODO: discuss
-        raise NotImplementedError
-
-    def get_cohesive_energy(self, material_id, per_atom=False):
-        """
-        Gets the cohesive for a material (eV per formula unit). Cohesive energy
-            is defined as the difference between the bulk energy and the sum of
-            total DFT energy of isolated atoms for atom elements in the bulk.
-        Args:
-            material_id (str): Materials Project material_id, e.g. 'mp-123'.
-            per_atom (bool): Whether or not to return cohesive energy per atom
-        Returns:
-            Cohesive energy (eV).
-        """
-        raise NotImplementedError
-
-    def get_reaction(self, reactants, products):
-        """
-        Gets a reaction from the Materials Project.
-
-        Args:
-            reactants ([str]): List of formulas
-            products ([str]): List of formulas
-
-        Returns:
-            rxn
-        """
-        raise NotImplementedError
-
     def get_substrates(self, material_id, orient=None):
         """
         Get a substrate list for a material id. The list is in order of
@@ -720,39 +751,3 @@ def get_gb_data(
                 rotation_axis=rotation_axis,
             )
         ]
-
-    def get_interface_reactions(
-        self,
-        reactant1,
-        reactant2,
-        open_el=None,
-        relative_mu=None,
-        use_hull_energy=False,
-    ):
-        """
-        Gets critical reactions between two reactants.
-
-        Get critical reactions ("kinks" in the mixing ratio where
-        reaction products change) between two reactants. See the
-        `pymatgen.analysis.interface_reactions` module for more info.
-
-        Args:
-            reactant1 (str): Chemical formula for reactant
-            reactant2 (str): Chemical formula for reactant
-            open_el (str): Element in reservoir available to system
-            relative_mu (float): Relative chemical potential of element in
-                reservoir with respect to pure substance. Must be non-positive.
-            use_hull_energy (bool): Whether to use the convex hull energy for a
-            given composition for the reaction energy calculation. If false,
-            the energy of the ground state structure will be preferred; if a
-            ground state can not be found for a composition, the convex hull
-            energy will be used with a warning message.
-
-        Returns:
-            list: list of dicts of form {ratio,energy,rxn} where `ratio` is the
-                reactant mixing ratio, `energy` is the reaction energy
-                in eV/atom, and `rxn` is a
-                `pymatgen.analysis.reaction_calculator.Reaction`.
-
-        """
-        raise NotImplementedError

src/mp_api/routes/__init__.py

@@ -8,7 +8,7 @@
 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, PhononImgRester
+from mp_api.routes.phonon.client import PhononRester
 from mp_api.routes.elasticity.client import ElasticityRester
 from mp_api.routes.thermo.client import ThermoRester
 from mp_api.routes.dielectric.client import DielectricRester

src/mp_api/routes/charge_density/client.py

@@ -77,7 +77,33 @@ def get_charge_density_calculation_ids_from_material_id(self, material_id: str):
 
         if len(calculation_ids) > 0:
             result = self.search(
-                task_ids=",".join(calculation_ids), fields=["task_id"], chunk_size=10
+                task_ids=",".join(calculation_ids),
+                fields=["task_id", "last_updated"],
+                chunk_size=10,
             )
 
         return result
+
+    def get_charge_density_from_material_id(self, material_id: str):
+        """
+        Get charge density data for a given Materials Project ID.
+
+        Arguments:
+            material_id (str): Material Project ID
+
+        Returns:
+            chgcar (dict): Pymatgen CHGCAR object.
+        """
+
+        task_id = sorted(
+            self.get_charge_density_calculation_ids_from_material_id(material_id),
+            key=lambda d: d["last_updated"],
+            reverse=True,
+        )[0]["task_id"]
+
+        result = self.search(task_ids=task_id, fields=["task_id", "data"], chunk_size=1)
+
+        if len(result) > 0:
+            return result[0]["data"]
+        else:
+            raise MPRestError("No charge density found")

src/mp_api/routes/dielectric/resources.py

@@ -13,9 +13,12 @@ def dielectric_resource(dielectric_store):
             DielectricQuery(),
             SortQuery(),
             PaginationQuery(),
-            SparseFieldsQuery(DielectricDoc, default_fields=["task_id", "last_updated"]),
+            SparseFieldsQuery(
+                DielectricDoc, default_fields=["task_id", "last_updated"]
+            ),
         ],
         tags=["Dielectric"],
+        monty_encoded_response=True,
     )
 
     return resource

src/mp_api/routes/dois/resources.py

@@ -14,6 +14,7 @@ def dois_resource(dois_store):
         ],
         tags=["DOIs"],
         enable_default_search=False,
+        monty_encoded_response=True,
     )
 
     return resource

src/mp_api/routes/elasticity/resources.py

@@ -21,9 +21,12 @@ def elasticity_resource(elasticity_store):
             PoissonQuery(),
             SortQuery(),
             PaginationQuery(),
-            SparseFieldsQuery(ElasticityDoc, default_fields=["task_id", "pretty_formula"],),
+            SparseFieldsQuery(
+                ElasticityDoc, default_fields=["task_id", "pretty_formula"],
+            ),
         ],
         tags=["Elasticity"],
+        monty_encoded_response=True,
     )
 
     return resource

src/mp_api/routes/electronic_structure/resources.py

@@ -33,6 +33,7 @@ def es_resource(es_store):
             ),
         ],
         tags=["Electronic Structure"],
+        monty_encoded_response=True,
     )
 
     return resource
@@ -54,6 +55,7 @@ def bs_resource(es_store):
         tags=["Electronic Structure"],
         enable_get_by_key=False,
         sub_path="/bandstructure/",
+        monty_encoded_response=True,
     )
 
     return resource
@@ -92,6 +94,7 @@ def dos_resource(es_store):
         tags=["Electronic Structure"],
         enable_get_by_key=False,
         sub_path="/dos/",
+        monty_encoded_response=True,
     )
 
     return resource

src/mp_api/routes/eos/resources.py

@@ -16,6 +16,7 @@ def eos_resource(eos_store):
             SparseFieldsQuery(EOSDoc, default_fields=["task_id"]),
         ],
         tags=["EOS"],
+        monty_encoded_response=True,
     )
 
     return resource