Deprecation data added to PropertyDoc (#247)

* Deprecated data added to property doc * kwargs added to relevant model class methods * Deprecated added to builders * Fix tests for deprecated data
materialsproject · Aug 19, 2021 · 380cfc3 · 380cfc3
1 parent eedcf9c
commit 380cfc3
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Showing 18 changed files with 116 additions and 195 deletions.
diff --git a/emmet-builders/emmet/builders/materials/electronic_structure.py b/emmet-builders/emmet/builders/materials/electronic_structure.py
@@ -160,6 +160,7 @@ def process_item(self, mat):
         # Default summary data
         d = dict(
             material_id=mat[self.materials.key],
+            deprecated=mat["deprecated"],
             task_id=mat["other"]["task_id"],
             structure=structure,
             band_gap=mat["other"]["band_gap"],
@@ -205,6 +206,7 @@ def process_item(self, mat):
                     dos=dos,
                     is_gap_direct=d["is_gap_direct"],
                     is_metal=d["is_metal"],
+                    deprecated=d["deprecated"],
                     **bs,
                 )
                 doc = self._bsdos_checks(doc, dos[mat["dos"]["task_id"]], structures)
@@ -316,6 +318,7 @@ def _update_materials_doc(self, mat_id):
                 "structure",
                 "inputs",
                 "task_types",
+                "deprecated",
                 self.materials.last_updated_field,
             ],
             criteria={self.materials.key: mat_id},

diff --git a/emmet-builders/emmet/builders/materials/oxidation_states.py b/emmet-builders/emmet/builders/materials/oxidation_states.py
@@ -32,16 +32,17 @@ def __init__(
         super().__init__(
             source=materials,
             target=oxidation_states,
-            projection=["structure"],
+            projection=["structure", "deprecated"],
             **kwargs,
         )
 
     def unary_function(self, item):
         structure = Structure.from_dict(item["structure"])
         mpid = item["material_id"]
+        deprecated = item["deprecated"]
 
         oxi_doc = OxidationStateDoc.from_structure(
-            structure=structure, material_id=mpid
+            structure=structure, material_id=mpid, deprecated=deprecated
         )
         doc = jsanitize(oxi_doc.dict(), allow_bson=True)
 

diff --git a/emmet-builders/emmet/builders/materials/robocrys.py b/emmet-builders/emmet/builders/materials/robocrys.py
@@ -26,17 +26,19 @@ def __init__(
             source=oxidation_states,
             target=robocrys,
             query=query,
-            projection=["material_id", "structure"],
+            projection=["material_id", "structure", "deprecated"],
             **kwargs
         )
 
     def unary_function(self, item):
         structure = Structure.from_dict(item["structure"])
         mpid = item["material_id"]
+        deprecated = item["deprecated"]
 
         doc = RobocrystallogapherDoc.from_structure(
             structure=structure,
             material_id=mpid,
+            deprecated=deprecated,
             fields=[],
         )
 

diff --git a/emmet-builders/emmet/builders/materials/substrates.py b/emmet-builders/emmet/builders/materials/substrates.py
@@ -83,13 +83,14 @@ def get_items(self):
             )
             mat = self.materials.query_one(
                 criteria={self.materials.key: mpid},
-                properties=["structure", "material_id", "last_updated"],
+                properties=["structure", "deprecated", "material_id", "last_updated"],
             )
 
             yield {
                 "structure": mat["structure"],
                 "material_id": mat[self.materials.key],
                 "elastic_tensor": e_tensor,
+                "deprecated": mat["deprecated"],
                 "last_updated": max(
                     mat.get("last_updated"), e_tensor.get("last_updated")
                 ),
@@ -111,6 +112,7 @@ def process_item(self, item):
         elastic_tensor = (
             ElasticTensor.from_voigt(elastic_tensor) if elastic_tensor else None
         )
+        deprecated = item["deprecated"]
 
         self.logger.debug("Calculating substrates for {}".format(item["task_id"]))
 
@@ -121,6 +123,7 @@ def process_item(self, item):
             material_id=mpid,
             structure=film,
             elastic_tensor=elastic_tensor,
+            deprecated=deprecated,
             last_updated=item["last_updated"],
         )
 

diff --git a/emmet-builders/emmet/builders/vasp/thermo.py b/emmet-builders/emmet/builders/vasp/thermo.py
@@ -150,7 +150,7 @@ def process_item(self, item: List[Dict]):
         self.logger.debug(f"{len(pd_entries)} remain in {chemsys} after filtering")
 
         try:
-            docs = ThermoDoc.from_entries(pd_entries)
+            docs = ThermoDoc.from_entries(pd_entries, deprecated=False)
             for doc in docs:
                 doc.entries = material_entries[doc.material_id]
                 doc.entry_types = list(material_entries[doc.material_id].keys())
@@ -228,7 +228,9 @@ def get_entries(self, chemsys: str) -> List[Dict]:
         new_q["chemsys"] = {"$in": list(query_chemsys)}
         new_q["deprecated"] = False
         materials_docs = list(
-            self.materials.query(criteria=new_q, properties=["material_id", "entries"])
+            self.materials.query(
+                criteria=new_q, properties=["material_id", "entries", "deprecated"]
+            )
         )
 
         # Get Oxidation state data for each material

diff --git a/emmet-core/emmet/core/electronic_structure.py b/emmet-core/emmet/core/electronic_structure.py
@@ -46,25 +46,19 @@ class ElectronicStructureSummary(ElectronicStructureBaseData):
 
     is_metal: bool = Field(..., description="Whether the material is a metal.")
 
-    magnetic_ordering: Union[str, Ordering] = Field(
-        ..., description="Magnetic ordering of the calculation."
-    )
+    magnetic_ordering: Union[str, Ordering] = Field(..., description="Magnetic ordering of the calculation.")
 
 
 class BandStructureSummaryData(ElectronicStructureSummary):
     nbands: float = Field(..., description="Number of bands.")
 
-    equivalent_labels: Dict = Field(
-        ..., description="Equivalent k-point labels in other k-path conventions."
-    )
+    equivalent_labels: Dict = Field(..., description="Equivalent k-point labels in other k-path conventions.")
 
     direct_gap: float = Field(..., description="Direct gap energy in eV.")
 
 
 class DosSummaryData(ElectronicStructureBaseData):
-    spin_polarization: float = Field(
-        None, description="Spin polarization at the fermi level."
-    )
+    spin_polarization: float = Field(None, description="Spin polarization at the fermi level.")
 
 
 class BandstructureData(BaseModel):
@@ -85,9 +79,7 @@ class BandstructureData(BaseModel):
 
 
 class DosData(BaseModel):
-    total: Dict[Union[Spin, str], DosSummaryData] = Field(
-        None, description="Total DOS summary data."
-    )
+    total: Dict[Union[Spin, str], DosSummaryData] = Field(None, description="Total DOS summary data.")
 
     elemental: Dict[
         Element,
@@ -108,9 +100,7 @@ class DosData(BaseModel):
         description="Band structure summary data using the Latimer-Munro path convention.",
     )
 
-    magnetic_ordering: Union[str, Ordering] = Field(
-        None, description="Magnetic ordering of the calculation."
-    )
+    magnetic_ordering: Union[str, Ordering] = Field(None, description="Magnetic ordering of the calculation.")
 
 
 T = TypeVar("T", bound="ElectronicStructureDoc")
@@ -121,11 +111,9 @@ class ElectronicStructureDoc(PropertyDoc, ElectronicStructureSummary):
     Definition for a core Electronic Structure Document
     """
 
-    property_name = "electronc_structure"
+    property_name = "electronic_structure"
 
-    bandstructure: BandstructureData = Field(
-        None, description="Band structure data for the material."
-    )
+    bandstructure: BandstructureData = Field(None, description="Band structure data for the material.")
 
     dos: DosData = Field(None, description="Density of states data for the material.")
 
@@ -145,6 +133,7 @@ def from_bsdos(  # type: ignore[override]
         setyawan_curtarolo: Dict[MPID, BandStructureSymmLine] = None,
         hinuma: Dict[MPID, BandStructureSymmLine] = None,
         latimer_munro: Dict[MPID, BandStructureSymmLine] = None,
+        **kwargs
     ) -> T:
         """
         Builds a electronic structure document using band structure and density of states data.
@@ -276,13 +265,9 @@ def from_bsdos(  # type: ignore[override]
                 bs_task, bs = list(bs_input.items())[0]
 
                 if structures is not None and structures[bs_task]:
-                    bs_mag_ordering = CollinearMagneticStructureAnalyzer(
-                        structures[bs_task]
-                    ).ordering
+                    bs_mag_ordering = CollinearMagneticStructureAnalyzer(structures[bs_task]).ordering
                 else:
-                    bs_mag_ordering = CollinearMagneticStructureAnalyzer(
-                        bs.structure
-                    ).ordering
+                    bs_mag_ordering = CollinearMagneticStructureAnalyzer(bs.structure).ordering
 
                 gap_dict = bs.get_band_gap()
                 is_metal = bs.is_metal()
@@ -313,26 +298,11 @@ def from_bsdos(  # type: ignore[override]
                 equivalent_labels = hskp.equiv_labels
 
                 if bs_type == "latimer_munro":
-                    gen_labels = set(
-                        [
-                            label
-                            for label in equivalent_labels["latimer_munro"][
-                                "setyawan_curtarolo"
-                            ]
-                        ]
-                    )
-                    kpath_labels = set(
-                        [
-                            kpoint.label
-                            for kpoint in bs.kpoints
-                            if kpoint.label is not None
-                        ]
-                    )
+                    gen_labels = set([label for label in equivalent_labels["latimer_munro"]["setyawan_curtarolo"]])
+                    kpath_labels = set([kpoint.label for kpoint in bs.kpoints if kpoint.label is not None])
 
                     if not gen_labels.issubset(kpath_labels):
-                        new_structure = SpacegroupAnalyzer(
-                            bs.structure
-                        ).get_primitive_standard_structure(
+                        new_structure = SpacegroupAnalyzer(bs.structure).get_primitive_standard_structure(
                             international_monoclinic=False
                         )
 
@@ -364,11 +334,7 @@ def from_bsdos(  # type: ignore[override]
 
         # Obtain summary data
 
-        bs_gap = (
-            bs_entry.setyawan_curtarolo.band_gap
-            if bs_entry.setyawan_curtarolo is not None
-            else None
-        )
+        bs_gap = bs_entry.setyawan_curtarolo.band_gap if bs_entry.setyawan_curtarolo is not None else None
         dos_cbm, dos_vbm = dos_obj.get_cbm_vbm()
         dos_gap = max(dos_cbm - dos_vbm, 0.0)
 
@@ -411,4 +377,5 @@ def from_bsdos(  # type: ignore[override]
             magnetic_ordering=summary_magnetic_ordering,
             bandstructure=bs_entry,
             dos=dos_entry,
+            **kwargs
         )
diff --git a/emmet-core/emmet/core/material_property.py b/emmet-core/emmet/core/material_property.py
@@ -2,14 +2,15 @@
 from __future__ import annotations
 
 from datetime import datetime
-from typing import Sequence, Type, TypeVar
+from typing import Sequence, Type, TypeVar, Union, List
 
 from pydantic import Field
 from pymatgen.core import Structure
 
 from emmet.core.material import PropertyOrigin
 from emmet.core.mpid import MPID
 from emmet.core.structure import StructureMetadata
+from emmet.core.vasp.validation import DeprecationMessage
 
 S = TypeVar("S", bound="PropertyDoc")
 
@@ -28,27 +29,28 @@ class PropertyDoc(StructureMetadata):
         "This comes in the form of an MPID or int",
     )
 
+    deprecated: bool = Field(
+        ...,
+        description="Whether this property document is deprecated.",
+    )
+
+    reasons: List[Union[DeprecationMessage, str]] = Field(
+        None, description="List of deprecation tags detailing why this document isn't valid"
+    )
+
     last_updated: datetime = Field(
         description="Timestamp for the most recent calculation update for this property",
         default_factory=datetime.utcnow,
     )
 
-    origins: Sequence[PropertyOrigin] = Field(
-        [], description="Dictionary for tracking the provenance of properties"
-    )
+    origins: Sequence[PropertyOrigin] = Field([], description="Dictionary for tracking the provenance of properties")
 
-    warnings: Sequence[str] = Field(
-        [], description="Any warnings related to this property"
-    )
+    warnings: Sequence[str] = Field([], description="Any warnings related to this property")
 
     @classmethod
-    def from_structure(  # type: ignore[override]
-        cls: Type[S], structure: Structure, material_id: MPID, **kwargs
-    ) -> S:
+    def from_structure(cls: Type[S], structure: Structure, material_id: MPID, **kwargs) -> S:  # type: ignore[override]
         """
         Builds a materials document using the minimal amount of information
         """
 
-        return super().from_structure(  # type: ignore
-            structure=structure, material_id=material_id, **kwargs
-        )
+        return super().from_structure(structure=structure, material_id=material_id, **kwargs)  # type: ignore
diff --git a/emmet-core/emmet/core/oxidation_states.py b/emmet-core/emmet/core/oxidation_states.py
@@ -18,15 +18,9 @@ class OxidationStateDoc(PropertyDoc):
 
     property_name = "oxidation"
 
-    possible_species: List[str] = Field(
-        description="Possible charged species in this material"
-    )
-    possible_valences: List[float] = Field(
-        description="List of valences for each site in this material"
-    )
-    average_oxidation_states: Dict[str, float] = Field(
-        description="Average oxidation states for each unique species"
-    )
+    possible_species: List[str] = Field(description="Possible charged species in this material")
+    possible_valences: List[float] = Field(description="List of valences for each site in this material")
+    average_oxidation_states: Dict[str, float] = Field(description="Average oxidation states for each unique species")
     method: str = Field(description="Method used to compute oxidation states")
 
     @classmethod
@@ -36,8 +30,7 @@ def from_structure(cls, structure: Structure, material_id: MPID, **kwargs):  # t
             bva = BVAnalyzer()
             valences = bva.get_valences(structure)
             possible_species = {
-                str(Specie(structure[idx].specie, oxidation_state=valence))
-                for idx, valence in enumerate(valences)
+                str(Specie(structure[idx].specie, oxidation_state=valence)) for idx, valence in enumerate(valences)
             }
 
             structure.add_oxidation_state_by_site(valences)
@@ -51,10 +44,7 @@ def from_structure(cls, structure: Structure, material_id: MPID, **kwargs):  # t
             for site in structure:
                 site_oxidation_list[site.specie.element].append(site.specie.oxi_state)
 
-            oxi_state_dict = {
-                str(el): np.mean(oxi_states)
-                for el, oxi_states in site_oxidation_list.items()
-            }
+            oxi_state_dict = {str(el): np.mean(oxi_states) for el, oxi_states in site_oxidation_list.items()}
 
             d = {
                 "possible_species": list(possible_species),
@@ -67,15 +57,10 @@ def from_structure(cls, structure: Structure, material_id: MPID, **kwargs):  # t
             logging.error("BVAnalyzer failed with: {}".format(e))
 
             try:
-                first_oxi_state_guess = structure.composition.oxi_state_guesses(
-                    max_sites=-50
-                )[0]
-                valences = [
-                    first_oxi_state_guess[site.species_string] for site in structure
-                ]
+                first_oxi_state_guess = structure.composition.oxi_state_guesses(max_sites=-50)[0]
+                valences = [first_oxi_state_guess[site.species_string] for site in structure]
                 possible_species = {
-                    str(Specie(el, oxidation_state=valence))
-                    for el, valence in first_oxi_state_guess.items()
+                    str(Specie(el, oxidation_state=valence)) for el, valence in first_oxi_state_guess.items()
                 }
 
                 structure.add_oxidation_state_by_site(valences)
@@ -92,9 +77,5 @@ def from_structure(cls, structure: Structure, material_id: MPID, **kwargs):  # t
                 raise e
 
         return super().from_structure(
-            structure=structure,
-            material_id=material_id,
-            include_structure=True,
-            **d,
-            **kwargs
+            structure=structure, material_id=material_id, include_structure=True, **d, **kwargs
         )