Provenance endpoint and test bug fixes (#346)

* Initial commit of prevenance endpoint

* Provenance client suffix fix

* Disable validation on provenance endpoint

* xas, and oxi test fixes

* Remove phonon_img endpoint from tests

* Fix provenance client stub

* Get references method added to MPRester

* Mark appropriate provenance test  xfail

app.py

@@ -42,6 +42,7 @@
 )
 molecules_store_json = os.environ.get("MOLECULES_STORE", "molecules_store.json")
 oxi_states_store_json = os.environ.get("OXI_STATES_STORE", "oxi_states_store.json")
+provenance_store_json = os.environ.get("PROVENANCE_STORE", "provenance_store.json")
 summary_store_json = os.environ.get("SUMMARY_STORE", "summary_store.json")
 
 es_store_json = os.environ.get("ES_STORE", "es_store.json")
@@ -222,6 +223,13 @@
         collection_name="oxi_states",
     )
 
+    provenance_store = MongoURIStore(
+        uri=f"mongodb+srv://{db_uri}",
+        database="mp_core",
+        key="material_id",
+        collection_name="provenance",
+    )
+
     summary_store = MongoURIStore(
         uri=f"mongodb+srv://{db_uri}",
         database="mp_core",
@@ -320,6 +328,7 @@
     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)
 
     es_store = loadfn(es_store_json)
@@ -479,6 +488,11 @@
 
 resources.update({"oxidation_states": [oxi_states_resource(oxi_states_store)]})
 
+# Provenance
+from mp_api.routes.provenance.resources import provenance_resource
+
+resources.update({"provenance": [provenance_resource(provenance_store)]})
+
 # Charge Density
 from mp_api.routes.charge_density.resources import charge_density_resource
 

src/mp_api/matproj.py

@@ -221,7 +221,7 @@ def get_materials_id_references(self, material_id):
         Returns:
             BibTeX (str)
         """
-        raise NotImplementedError
+        return self.provenance.get_document_by_id(material_id).references
 
     def get_materials_ids(self, chemsys_formula):
         """

src/mp_api/routes/__init__.py

@@ -27,3 +27,4 @@
     DosRester,
 )
 from mp_api.routes.oxidation_states.client import OxidationStatesRester
+from mp_api.routes.provenance.client import ProvenanceRester

src/mp_api/routes/provenance/client.py

@@ -0,0 +1,9 @@
+from mp_api.core.client import BaseRester
+from emmet.core.provenance import ProvenanceDoc
+
+
+class ProvenanceRester(BaseRester):
+
+    suffix = "provenance"
+    document_model = ProvenanceDoc  # type: ignore
+    primary_key = "material_id"

src/mp_api/routes/provenance/client.pyi

@@ -0,0 +1,12 @@
+from typing import List, Optional
+from emmet.core.provenance import ProvenanceDoc
+
+
+class ProvenanceRester:
+
+    def get_document_by_id(
+        self,
+        document_id: str,
+        fields: Optional[List[str]] = None,
+        monty_decode: bool = True,
+    ) -> ProvenanceDoc: ...

src/mp_api/routes/provenance/resources.py

@@ -0,0 +1,17 @@
+from maggma.api.resource import ReadOnlyResource
+from maggma.api.query_operator import PaginationQuery
+
+from emmet.core.provenance import ProvenanceDoc
+
+
+def provenance_resource(provenance_store):
+    resource = ReadOnlyResource(
+        provenance_store,
+        ProvenanceDoc,
+        query_operators=[PaginationQuery()],
+        tags=["Provenance"],
+        disable_validation=True,
+        enable_default_search=False,
+    )
+
+    return resource

src/mp_api/routes/xas/client.py

@@ -8,7 +8,7 @@ class XASRester(BaseRester):
 
     suffix = "xas"
     document_model = XASDoc  # type: ignore
-    primary_key = "xas_id"
+    primary_key = "spectrum_id"
 
     def get_available_elements(
         # TODO implement actual check

tests/test_client.py

@@ -6,7 +6,6 @@
 
 key_only_resters = {
     "phonon": "mp-11703",
-    "phonon_img": "mp-11703",
     "similarity": "mp-149",
     "doi": "mp-149",
     "wulff": "mp-149",
@@ -20,15 +19,13 @@
     "electronic_structure_dos",
     "substrates",
     "synthesis",
-    "xas",  # Temp
 ]
 
 special_resters = [
-    "phonon_img",
     "charge_density",
 ]
 
-ignore_generic = ["oxidation_states"]
+ignore_generic = ["provenance"]  # temp
 
 
 mpr = MPRester()

tests/test_mprester.py

@@ -54,10 +54,10 @@ def test_get_database_version(self, mpr):
     def test_get_materials_id_from_task_id(self, mpr):
         assert mpr.get_materials_id_from_task_id("mp-540081") == "mp-19017"
 
-    # TODO: add method to MPRester
-    # def test_get_materials_id_references(self, mpr):
-    #     data = mpr.get_materials_id_references("mp-123")
-    #     assert len(data) > 1000
+    @pytest.mark.xfail
+    def test_get_materials_id_references(self, mpr):
+        data = mpr.get_materials_id_references("mp-123")
+        assert len(data) > 5
 
     def test_get_materials_ids_doc(self, mpr):
         mpids = mpr.get_materials_ids("Al2O3")