Remove single ID endpoints (#935)

* Remove get by key disable

* Fix eos

* Fix gb

* Fix similarity

* Fix dois

* Fix fermi

* Fix xas

* Fix phonon

* Fix surface props

* Fix electrodes doc position

* Fix robocrys docs

* More doc fixes

* Fix robocrys tags

* Fix doi endpoint key

* Rename grain_boundaries

* Fix XAS query op test

* More xps test fixes

* Typo

* Temp skip matminer related builders tests

* Fix pytest marks

* Comment out tests

emmet-api/emmet/api/core/documentation.py

@@ -190,7 +190,7 @@
             Project database. See the `SurfacePropDoc` schema for a full list of fields returned by this route.",
     },
     {
-        "name": "Robocrystallographer",
+        "name": "Materials Robocrystallographer",
         "description": "Route providing a computed text description for a material following the \
             methodology discussed by [Ganose *et al.*](https://doi.org/10.1557/mrc.2019.94) \
             Note that descriptions may not been calculated for all materials in the Materials \
@@ -204,11 +204,12 @@
             Project database. See the `SynthesisSearchResultModel` schema for a full list of fields returned by this route.",
     },
     {
-        "name": "Electrodes",
+        "name": "Materials Electrodes",
         "description": "Route providing computed electrode data for a material following the \
             methodology discussed by [Shen *et al.*](https://doi.org/10.1038/s41524-020-00422-3) \
             Note that electrode data has not been calculated for all materials in the Materials \
-            Project database. See the `InsertionElectrodeDoc` schema for a full list of fields returned by this route.",
+            Project database. See the `InsertionElectrodeDoc` and `ConversionElectrodeDoc` schema \
+            for a full list of fields returned by this route.",
     },
     {
         "name": "Materials Oxidation States",
@@ -238,6 +239,10 @@
         "belong to, following the methodolgy discussed by "
         "[Woods-Robinson, Horton and Persson](https://arxiv.org/pdf/2206.10715).",
     },
+    {
+        "name": "Materials Bonds",
+        "description": "Route for retrevial of bonding information for a given material.",
+    },
     {
         "name": "MPComplete",
         "description": "Route for submitting structures to the Materials Project. If calculations are run with the \

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

@@ -1,5 +1,6 @@
 from maggma.api.resource import ReadOnlyResource
 from emmet.core.dois import DOIDoc
+from emmet.api.routes.materials.materials.query_operators import MultiMaterialIDQuery
 from emmet.api.core.global_header import GlobalHeaderProcessor
 from maggma.api.query_operator import PaginationQuery, SparseFieldsQuery
 from emmet.api.core.settings import MAPISettings
@@ -10,14 +11,14 @@ def dois_resource(dois_store):
         dois_store,
         DOIDoc,
         query_operators=[
+            MultiMaterialIDQuery(),
             PaginationQuery(),
-            SparseFieldsQuery(DOIDoc, default_fields=["task_id", "doi"]),
+            SparseFieldsQuery(DOIDoc, default_fields=["material_id", "doi"]),
         ],
         header_processor=GlobalHeaderProcessor(),
         tags=["DOIs"],
-        enable_default_search=False,
         disable_validation=True,
-        timeout=MAPISettings().TIMEOUT,
+        timeout=MAPISettings().TIMEOUT,  # type: ignore
     )
 
     return resource

emmet-api/emmet/api/routes/materials/charge_density/resources.py

@@ -20,7 +20,6 @@ def charge_density_resource(s3_store):
         tags=["Materials Charge Density"],
         sub_path="/charge_density/",
         enable_default_search=True,
-        enable_get_by_key=False,
         disable_validation=True,
         query_disk_use=False,
     )

emmet-api/emmet/api/routes/materials/electronic_structure/resources.py

@@ -66,7 +66,6 @@ def bs_resource(es_store):
         ],
         header_processor=GlobalHeaderProcessor(),
         tags=["Materials Electronic Structure"],
-        enable_get_by_key=False,
         sub_path="/electronic_structure/bandstructure/",
         disable_validation=True,
         timeout=timeout,
@@ -85,7 +84,6 @@ def bs_obj_resource(s3_store):
         ],
         header_processor=GlobalHeaderProcessor(),
         tags=["Materials Electronic Structure"],
-        enable_get_by_key=False,
         enable_default_search=True,
         sub_path="/electronic_structure/bandstructure/object/",
         query_disk_use=False,
@@ -109,7 +107,6 @@ def dos_resource(es_store):
         ],
         header_processor=GlobalHeaderProcessor(),
         tags=["Materials Electronic Structure"],
-        enable_get_by_key=False,
         sub_path="/electronic_structure/dos/",
         disable_validation=True,
         timeout=timeout,
@@ -128,7 +125,6 @@ def dos_obj_resource(s3_store):
         ],
         header_processor=GlobalHeaderProcessor(),
         tags=["Materials Electronic Structure"],
-        enable_get_by_key=False,
         enable_default_search=True,
         sub_path="/electronic_structure/dos/object/",
         query_disk_use=False,

emmet-api/emmet/api/routes/materials/eos/resources.py

@@ -1,5 +1,6 @@
 from maggma.api.resource import ReadOnlyResource
 from emmet.core.eos import EOSDoc
+from emmet.api.routes.materials.materials.query_operators import MultiMaterialIDQuery
 
 from maggma.api.query_operator import PaginationQuery, SparseFieldsQuery
 from emmet.api.core.global_header import GlobalHeaderProcessor
@@ -11,6 +12,7 @@ def eos_resource(eos_store):
         eos_store,
         EOSDoc,
         query_operators=[
+            MultiMaterialIDQuery(),
             PaginationQuery(),
             SparseFieldsQuery(EOSDoc, default_fields=["task_id"]),
         ],

emmet-api/emmet/api/routes/materials/fermi/resources.py

@@ -1,5 +1,6 @@
 from maggma.api.resource import ReadOnlyResource
 from emmet.core.fermi import FermiDoc
+from emmet.api.routes.materials.materials.query_operators import MultiMaterialIDQuery
 from emmet.api.core.global_header import GlobalHeaderProcessor
 from maggma.api.query_operator import PaginationQuery, SparseFieldsQuery
 
@@ -9,6 +10,7 @@ def fermi_resource(fermi_store):
         fermi_store,
         FermiDoc,
         query_operators=[
+            MultiMaterialIDQuery(),
             PaginationQuery(),
             SparseFieldsQuery(FermiDoc, default_fields=["task_id", "last_updated"]),
         ],

emmet-api/emmet/api/routes/materials/grain_boundary/resources.py

@@ -5,6 +5,7 @@
     GBStructureQuery,
     GBTaskIDQuery,
 )
+from emmet.api.routes.materials.materials.query_operators import MultiMaterialIDQuery
 from maggma.api.query_operator import (
     PaginationQuery,
     SparseFieldsQuery,
@@ -19,6 +20,7 @@ def gb_resource(gb_store):
         gb_store,
         GrainBoundaryDoc,
         query_operators=[
+            MultiMaterialIDQuery(),
             GBTaskIDQuery(),
             NumericQuery(
                 model=GrainBoundaryDoc, excluded_fields=["rotation_axis", "gb_plane"]
@@ -31,10 +33,9 @@ def gb_resource(gb_store):
         ],
         header_processor=GlobalHeaderProcessor(),
         tags=["Materials Grain Boundaries"],
-        sub_path="/grain_boundary/",
-        enable_get_by_key=False,
+        sub_path="/grain_boundaries/",
         disable_validation=True,
-        timeout=MAPISettings().TIMEOUT,
+        timeout=MAPISettings().TIMEOUT,  # type: ignore
     )
 
     return resource

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

@@ -29,7 +29,7 @@
 from emmet.api.core.global_header import GlobalHeaderProcessor
 from emmet.api.core.settings import MAPISettings
 
-timeout = MAPISettings().TIMEOUT
+timeout = MAPISettings().TIMEOUT  # type: ignore
 
 
 def find_structure_resource(materials_store):
@@ -90,9 +90,8 @@ def blessed_tasks_resource(materials_store):
         header_processor=GlobalHeaderProcessor(),
         tags=["Materials"],
         sub_path="/core/blessed_tasks/",
-        enable_get_by_key=False,
         disable_validation=True,
-        timeout=MAPISettings().TIMEOUT,
+        timeout=MAPISettings().TIMEOUT,  # type: ignore
     )
 
     return resource
@@ -122,7 +121,7 @@ def materials_resource(materials_store):
         tags=["Materials"],
         sub_path="/core/",
         disable_validation=True,
-        timeout=MAPISettings().TIMEOUT,
+        timeout=MAPISettings().TIMEOUT,  # type: ignore
     )
 
     return resource

emmet-api/emmet/api/routes/materials/phonon/resources.py

@@ -2,6 +2,7 @@
 from maggma.api.resource import ReadOnlyResource
 
 from emmet.core.phonon import PhononBSDOSDoc
+from emmet.api.routes.materials.materials.query_operators import MultiMaterialIDQuery
 from emmet.api.core.global_header import GlobalHeaderProcessor
 from emmet.api.core.settings import MAPISettings
 
@@ -11,17 +12,17 @@ def phonon_bsdos_resource(phonon_bs_store):
         phonon_bs_store,
         PhononBSDOSDoc,
         query_operators=[
+            MultiMaterialIDQuery(),
             PaginationQuery(),
             SparseFieldsQuery(
-                PhononBSDOSDoc, default_fields=["task_id", "last_updated"]
+                PhononBSDOSDoc, default_fields=["material_id", "last_updated"]
             ),
         ],
         header_processor=GlobalHeaderProcessor(),
         tags=["Materials Phonon"],
         sub_path="/phonon/",
-        enable_default_search=False,
         disable_validation=True,
-        timeout=MAPISettings().TIMEOUT,
+        timeout=MAPISettings().TIMEOUT,  # type: ignore
     )
 
     return resource

emmet-api/emmet/api/routes/materials/robocrys/resources.py

@@ -37,9 +37,9 @@ def robo_search_resource(robo_store):
         robo_store,
         RobocrystallogapherDoc,
         pipeline_query_operator=RoboTextSearchQuery(),
-        tags=["Robocrystallographer"],
         sub_path="/robocrys/text_search/",
         header_processor=GlobalHeaderProcessor(),
+        tags=["Materials Robocrystallographer"],
         timeout=timeout,
     )
 

emmet-api/emmet/api/routes/materials/similarity/resources.py

@@ -2,6 +2,7 @@
 from maggma.api.resource import ReadOnlyResource
 from emmet.api.core.global_header import GlobalHeaderProcessor
 from emmet.api.core.settings import MAPISettings
+from emmet.api.routes.materials.materials.query_operators import MultiMaterialIDQuery
 
 from emmet.core.similarity import SimilarityDoc
 
@@ -11,15 +12,15 @@ def similarity_resource(similarity_store):
         similarity_store,
         SimilarityDoc,
         query_operators=[
+            MultiMaterialIDQuery(),
             PaginationQuery(),
             SparseFieldsQuery(SimilarityDoc, default_fields=["material_id"]),
         ],
         header_processor=GlobalHeaderProcessor(),
         tags=["Materials Similarity"],
         sub_path="/similarity/",
-        enable_default_search=False,
         disable_validation=True,
-        timeout=MAPISettings().TIMEOUT,
+        timeout=MAPISettings().TIMEOUT,  # type: ignore
     )
 
     return resource

emmet-api/emmet/api/routes/materials/substrates/resources.py

@@ -30,7 +30,6 @@ def substrates_resource(substrates_store):
         header_processor=GlobalHeaderProcessor(),
         tags=["Materials Substrates"],
         sub_path="/substrates/",
-        enable_get_by_key=False,
         disable_validation=True,
         timeout=MAPISettings().TIMEOUT,
     )

emmet-api/emmet/api/routes/materials/surface_properties/resources.py

@@ -4,6 +4,7 @@
 from emmet.api.core.settings import MAPISettings
 
 from emmet.api.core.global_header import GlobalHeaderProcessor
+from emmet.api.routes.materials.materials.query_operators import MultiMaterialIDQuery
 from emmet.api.routes.materials.surface_properties.query_operators import (
     ReconstructedQuery,
 )
@@ -15,6 +16,7 @@ def surface_props_resource(surface_prop_store):
         surface_prop_store,
         SurfacePropDoc,
         query_operators=[
+            MultiMaterialIDQuery(),
             NumericQuery(model=SurfacePropDoc),
             ReconstructedQuery(),
             PaginationQuery(),
@@ -24,7 +26,7 @@ def surface_props_resource(surface_prop_store):
         tags=["Materials Surface Properties"],
         sub_path="/surface_properties/",
         disable_validation=True,
-        timeout=MAPISettings().TIMEOUT,
+        timeout=MAPISettings().TIMEOUT,  # type: ignore
     )
 
     return resource

emmet-api/emmet/api/routes/materials/tasks/resources.py

@@ -54,7 +54,6 @@ def task_deprecation_resource(materials_store):
         DeprecationDoc,
         query_operators=[DeprecationQuery(), PaginationQuery()],
         tags=["Materials Tasks"],
-        enable_get_by_key=False,
         enable_default_search=True,
         sub_path="/tasks/deprecation/",
         header_processor=GlobalHeaderProcessor(),

emmet-api/emmet/api/routes/materials/xas/query_operators.py

@@ -30,26 +30,26 @@ def ensure_indexes(self):  # pragma: no cover
         return [(key, False) for key in keys]
 
 
-class XASTaskIDQuery(QueryOperator):
+class XASIDQuery(QueryOperator):
     """
-    Method to generate a query for XAS data given a list of task_ids
+    Method to generate a query for XAS data given a list of spectrum_ids
     """
 
     def query(
         self,
-        material_ids: Optional[str] = Query(
-            None, description="Comma-separated list of material_id to query on"
+        spectrum_ids: Optional[str] = Query(
+            None, description="Comma-separated list of spectrum_id to query on"
         ),
     ) -> STORE_PARAMS:
         crit = {}
 
-        if material_ids:
+        if spectrum_ids:
             crit.update(
                 {
-                    "material_id": {
+                    "spectrum_id": {
                         "$in": [
-                            material_id.strip()
-                            for material_id in material_ids.split(",")
+                            spectrum_id.strip()
+                            for spectrum_id in spectrum_ids.split(",")
                         ]
                     }
                 }

emmet-api/emmet/api/routes/materials/xas/resources.py

@@ -2,13 +2,14 @@
 from emmet.core.xas import XASDoc
 
 from maggma.api.query_operator import PaginationQuery, SparseFieldsQuery
+from emmet.api.routes.materials.materials.query_operators import MultiMaterialIDQuery
 from emmet.api.routes.materials.materials.query_operators import (
     ElementsQuery,
     FormulaQuery,
     ChemsysQuery,
 )
 from emmet.api.core.global_header import GlobalHeaderProcessor
-from emmet.api.routes.materials.xas.query_operators import XASQuery, XASTaskIDQuery
+from emmet.api.routes.materials.xas.query_operators import XASQuery, XASIDQuery
 from emmet.api.core.settings import MAPISettings
 
 
@@ -17,11 +18,12 @@ def xas_resource(xas_store):
         xas_store,
         XASDoc,
         query_operators=[
+            MultiMaterialIDQuery(),
             FormulaQuery(),
             ChemsysQuery(),
             ElementsQuery(),
             XASQuery(),
-            XASTaskIDQuery(),
+            XASIDQuery(),
             PaginationQuery(),
             SparseFieldsQuery(
                 XASDoc,
@@ -40,7 +42,7 @@ def xas_resource(xas_store):
         tags=["Materials XAS"],
         sub_path="/xas/",
         disable_validation=True,
-        timeout=MAPISettings().TIMEOUT,
+        timeout=MAPISettings().TIMEOUT,  # type: ignore
     )
 
     return resource

emmet-api/emmet/api/routes/molecules/tasks/resources.py

@@ -53,7 +53,6 @@ def task_deprecation_resource(task_store):
         DeprecationDoc,
         query_operators=[DeprecationQuery(), PaginationQuery()],
         tags=["Molecules Tasks"],
-        enable_get_by_key=False,
         enable_default_search=True,
         sub_path="/tasks/deprecation/",
         header_processor=GlobalHeaderProcessor(),

emmet-api/material_resources.py

@@ -6,7 +6,7 @@
 
 resources = {}
 
-default_settings = MAPISettings()
+default_settings = MAPISettings()  # type: ignore
 
 db_uri = os.environ.get("MPCONTRIBS_MONGO_HOST", None)
 db_version = default_settings.DB_VERSION
@@ -136,7 +136,7 @@
     )
 
     doi_store = MongoURIStore(
-        uri=db_uri, database="mp_core", key="task_id", collection_name="dois"
+        uri=db_uri, database="mp_core", key="material_id", collection_name="dois"
     )
 
     substrates_store = MongoURIStore(