Merge pull request #364 from materialsproject/alloys

Alloys integration

emmet-api/app.py

@@ -13,206 +13,218 @@
 db_suffix = os.environ.get("MAPI_DB_NAME_SUFFIX", db_version)
 debug = default_settings.DEBUG
 
+# allow db_uri to be set with a different protocol scheme
+# but prepend with mongodb+srv:// if not otherwise specified
+if not urlparse(db_uri).scheme:
+    db_uri = "mongodb+srv://" + db_uri
+
 if db_uri:
 
     materials_store = MongoURIStore(
-        uri=f"mongodb+srv://{db_uri}",
+        uri=db_uri,
         database=f"mp_core_{db_suffix}",
         key="material_id",
         collection_name="materials",
     )
 
     bonds_store = MongoURIStore(
-        uri=f"mongodb+srv://{db_uri}",
+        uri=db_uri,
         database=f"mp_core_{db_suffix}",
         key="material_id",
         collection_name="bonds",
     )
 
     formula_autocomplete_store = MongoURIStore(
-        uri=f"mongodb+srv://{db_uri}",
+        uri=db_uri,
         database="mp_core",
         key="_id",
         collection_name="formula_autocomplete",
     )
 
     task_store = MongoURIStore(
-        uri=f"mongodb+srv://{db_uri}",
+        uri=db_uri,
         database="mp_core",
         key="task_id",
         collection_name="tasks",
     )
 
     thermo_store = MongoURIStore(
-        uri=f"mongodb+srv://{db_uri}",
+        uri=db_uri,
         database=f"mp_core_{db_suffix}",
         key="material_id",
         collection_name="thermo",
     )
 
     phase_diagram_store = MongoURIStore(
-        uri=f"mongodb+srv://{db_uri}",
+        uri=db_uri,
         database=f"mp_core_{db_suffix}",
         key="chemsys",
         collection_name="phase_diagram",
     )
 
     dielectric_store = MongoURIStore(
-        uri=f"mongodb+srv://{db_uri}",
+        uri=db_uri,
         database=f"mp_core_{db_suffix}",
         key="material_id",
         collection_name="dielectric",
     )
 
     piezoelectric_store = MongoURIStore(
-        uri=f"mongodb+srv://{db_uri}",
+        uri=db_uri,
         database=f"mp_core_{db_suffix}",
         key="material_id",
         collection_name="piezoelectric",
     )
 
     magnetism_store = MongoURIStore(
-        uri=f"mongodb+srv://{db_uri}",
+        uri=db_uri,
         database=f"mp_core_{db_suffix}",
         key="material_id",
         collection_name="magnetism",
     )
 
     phonon_bs_store = MongoURIStore(
-        uri=f"mongodb+srv://{db_uri}",
+        uri=db_uri,
         database="mp_core",
         key="material_id",
         collection_name="pmg_ph_bs",
     )
 
     eos_store = MongoURIStore(
-        uri=f"mongodb+srv://{db_uri}",
+        uri=db_uri,
         database="mp_core",
         key="task_id",
         collection_name="eos",
     )
 
     similarity_store = MongoURIStore(
-        uri=f"mongodb+srv://{db_uri}",
+        uri=db_uri,
         database="mp_core",
         key="material_id",
         collection_name="similarity",
     )
 
     xas_store = MongoURIStore(
-        uri=f"mongodb+srv://{db_uri}",
+        uri=db_uri,
         database="mp_core",
         key="spectrum_id",
         collection_name="xas",
     )
 
     gb_store = MongoURIStore(
-        uri=f"mongodb+srv://{db_uri}",
+        uri=db_uri,
         database="mp_core",
         key="task_id",
         collection_name="grain_boundaries",
     )
 
     fermi_store = MongoURIStore(
-        uri=f"mongodb+srv://{db_uri}",
+        uri=db_uri,
         database="mp_core",
         key="task_id",
         collection_name="fermi_surface",
     )
 
     elasticity_store = MongoURIStore(
-        uri=f"mongodb+srv://{db_uri}",
+        uri=db_uri,
         database="mp_core",
         key="task_id",
         collection_name="elasticity",
     )
 
     doi_store = MongoURIStore(
-        uri=f"mongodb+srv://{db_uri}",
+        uri=db_uri,
         database="mp_core",
         key="task_id",
         collection_name="dois",
     )
 
     substrates_store = MongoURIStore(
-        uri=f"mongodb+srv://{db_uri}",
+        uri=db_uri,
         database="mp_core",
         key="film_id",
         collection_name="substrates",
     )
 
     surface_props_store = MongoURIStore(
-        uri=f"mongodb+srv://{db_uri}",
+        uri=db_uri,
         database="mp_core",
         key="task_id",
         collection_name="surface_properties",
     )
 
     robo_store = MongoURIStore(
-        uri=f"mongodb+srv://{db_uri}",
+        uri=db_uri,
         database=f"mp_core_{db_suffix}",
         key="material_id",
         collection_name="robocrys",
     )
 
     synth_store = MongoURIStore(
-        uri=f"mongodb+srv://{db_uri}",
+        uri=db_uri,
         database="mp_core",
         key="_id",
         collection_name="synth_descriptions",
     )
 
     insertion_electrodes_store = MongoURIStore(
-        uri=f"mongodb+srv://{db_uri}",
+        uri=db_uri,
         database=f"mp_core_{db_suffix}",
         key="battery_id",
         collection_name="insertion_electrodes",
     )
 
     molecules_store = MongoURIStore(
-        uri=f"mongodb+srv://{db_uri}",
+        uri=db_uri,
         database="mp_core",
         key="task_id",
         collection_name="molecules",
     )
 
     oxi_states_store = MongoURIStore(
-        uri=f"mongodb+srv://{db_uri}",
+        uri=db_uri,
         database=f"mp_core_{db_suffix}",
         key="material_id",
         collection_name="oxi_states",
     )
 
     provenance_store = MongoURIStore(
-        uri=f"mongodb+srv://{db_uri}",
+        uri=db_uri,
         database=f"mp_core_{db_suffix}",
         key="material_id",
         collection_name="provenance",
     )
 
+    alloy_pairs_store = MongoURIStore(
+        uri=db_uri,
+        database=f"mp_core_{db_suffix}",
+        key="material_id",
+        collection_name="summary",
+    )
+
     summary_store = MongoURIStore(
-        uri=f"mongodb+srv://{db_uri}",
+        uri=db_uri,
         database=f"mp_core_{db_suffix}",
         key="material_id",
         collection_name="summary",
     )
 
     es_store = MongoURIStore(
-        uri=f"mongodb+srv://{db_uri}",
+        uri=db_uri,
         database=f"mp_core_{db_suffix}",
         key="material_id",
         collection_name="electronic_structure",
     )
 
     s3_bs_index = MongoURIStore(
-        uri=f"mongodb+srv://{db_uri}",
+        uri=db_uri,
         database="mp_core",
         key="fs_id",
         collection_name="s3_bandstructure_index",
     )
 
     s3_dos_index = MongoURIStore(
-        uri=f"mongodb+srv://{db_uri}",
+        uri=db_uri,
         database="mp_core",
         key="fs_id",
         collection_name="s3_dos_index",
@@ -237,7 +249,7 @@
     )
 
     s3_chgcar_index = MongoURIStore(
-        uri=f"mongodb+srv://{db_uri}",
+        uri=db_uri,
         database="mp_core",
         key="fs_id",
         collection_name="atomate_chgcar_fs_index",
@@ -254,34 +266,34 @@
     )
 
     chgcar_url = MongoURIStore(
-        uri=f"mongodb+srv://{db_uri}",
+        uri=db_uri,
         database="mp_core",
         key="fs_id",
         collection_name="chgcar_s3_urls",
     )
 
     mpcomplete_store = MongoURIStore(
-        uri=f"mongodb+srv://{db_uri}",
+        uri=db_uri,
         database="mp_consumers",
         key="submission_id",
         collection_name="mpcomplete",
     )
 
     consumer_settings_store = MongoURIStore(
-        uri=f"mongodb+srv://{db_uri}",
+        uri=db_uri,
         database="mp_consumers",
         key="consumer_id",
         collection_name="settings",
     )
 
     general_store = MongoURIStore(
-        uri=f"mongodb+srv://{db_uri}",
+        uri=db_uri,
         database="mp_consumers",
         key="submission_id",
         collection_name="general_store",
     )
 else:
-    raise RuntimeError("Must specify MongoDB Atlas URI")
+    raise RuntimeError("Must specify MongoDB URI containing inputs.")
 
 # Materials
 from emmet.api.routes.materials.resources import (

emmet-api/emmet/api/routes/alloys/query_operators.py

@@ -0,0 +1,63 @@
+from typing import Optional
+from fastapi import Query
+from maggma.api.query_operator import QueryOperator
+from maggma.api.utils import STORE_PARAMS
+
+from collections import defaultdict
+
+
+class MaterialIDsSearchQuery(QueryOperator):
+    """
+    Method to generate a query on search docs using multiple material_id values
+    """
+
+    def query(
+        self,
+        material_ids: Optional[str] = Query(
+            None, description="Comma-separated list of material_ids to query on"
+        ),
+    ) -> STORE_PARAMS:
+
+        crit = {}
+
+        if material_ids:
+
+            terminal_search = {
+                "_search.id": {
+                    "$in": [material_id.strip() for material_id in material_ids.split(",")]
+                }
+            }
+
+            member_search = {
+                "_search.member_ids": {
+                    "$in": [material_id.strip() for material_id in material_ids.split(",")]
+                }
+            }
+
+            crit.update({"$or": [terminal_search, member_search]})
+
+        return {"criteria": crit}
+
+
+class FormulaSearchQuery(QueryOperator):
+
+    def query(
+        self,
+        formulae: Optional[str] = Query(
+            None, description="Comma-separated list of end-point formulas to query."
+        ),
+    ) -> STORE_PARAMS:
+
+        crit = {}
+
+        if formulae:
+
+            formula_search = {
+                "_search.formula": {
+                    "$in": [formula.strip() for formula in formulae.split(",")]
+                }
+            }
+
+            crit.update(formula_search)
+
+        return {"criteria": crit}

emmet-api/emmet/api/routes/alloys/resources.py

@@ -0,0 +1,28 @@
+from maggma.api.resource import ReadOnlyResource
+
+from maggma.api.query_operator import PaginationQuery, SortQuery, SparseFieldsQuery
+
+from emmet.core.alloys import AlloyPairDoc, AlloySystemDoc
+
+from mp_api.routes.alloys.query_operators import (
+    MaterialIDsSearchQuery,
+    FormulaSearchQuery,
+)
+
+
+def alloys_resource(alloys_store):
+    resource = ReadOnlyResource(
+        alloy_pairs_store,
+        AlloyPairDoc,
+        query_operators=[
+            MaterialIDsSearchQuery(),
+            FormulaSearchQuery(),
+            SortQuery(),
+            PaginationQuery(),
+            SparseFieldsQuery(AlloyPairDoc, default_fields=["pair_id"],),
+        ],
+        tags=["Alloys"],
+        disable_validation=True,
+    )
+
+    return resource