nmdc-runtime 1.5.0__py3-none-any.whl → 1.7.0__py3-none-any.whl

nmdc_runtime/site/resources.py

@@ -19,7 +19,6 @@ from frozendict import frozendict
 from linkml_runtime.dumpers import json_dumper
 from pydantic import BaseModel, AnyUrl
 from pymongo import MongoClient, ReplaceOne, InsertOne
-from terminusdb_client import WOQLClient
 from toolz import get_in
 from toolz import merge
 
@@ -372,16 +371,37 @@ def gold_api_client_resource(context: InitResourceContext):
 
 @dataclass
 class NmdcPortalApiClient:
+
     base_url: str
-    # Using a cookie for authentication is not ideal and should be replaced
-    # when this API has an another authentication method
-    session_cookie: str
+    refresh_token: str
+    access_token: Optional[str] = None
+    access_token_expires_at: Optional[datetime] = None
+
+    def _request(self, method: str, endpoint: str, **kwargs):
+        r"""
+        Submits a request to the specified API endpoint;
+        after refreshing the access token, if necessary.
+        """
+        if self.access_token is None or datetime.now() > self.access_token_expires_at:
+            refresh_response = requests.post(
+                f"{self.base_url}/auth/refresh",
+                json={"refresh_token": self.refresh_token},
+            )
+            refresh_response.raise_for_status()
+            refresh_body = refresh_response.json()
+            self.access_token_expires_at = datetime.now() + timedelta(
+                seconds=refresh_body["expires_in"]
+            )
+            self.access_token = refresh_body["access_token"]
 
-    def fetch_metadata_submission(self, id: str) -> Dict[str, Any]:
-        response = requests.get(
-            f"{self.base_url}/api/metadata_submission/{id}",
-            cookies={"session": self.session_cookie},
+        headers = kwargs.get("headers", {})
+        headers["Authorization"] = f"Bearer {self.access_token}"
+        return requests.request(
+            method, f"{self.base_url}{endpoint}", **kwargs, headers=headers
         )
+
+    def fetch_metadata_submission(self, id: str) -> Dict[str, Any]:
+        response = self._request("GET", f"/api/metadata_submission/{id}")
         response.raise_for_status()
         return response.json()
 
@@ -389,13 +409,13 @@ class NmdcPortalApiClient:
 @resource(
     config_schema={
         "base_url": StringSource,
-        "session_cookie": StringSource,
+        "refresh_token": StringSource,
     }
 )
 def nmdc_portal_api_client_resource(context: InitResourceContext):
     return NmdcPortalApiClient(
         base_url=context.resource_config["base_url"],
-        session_cookie=context.resource_config["session_cookie"],
+        refresh_token=context.resource_config["refresh_token"],
     )
 
 
@@ -512,33 +532,3 @@ def get_mongo(run_config: frozendict):
         )
     )
     return mongo_resource(resource_context)
-
-
-class TerminusDB:
-    def __init__(self, server_url, user, key, account, dbid):
-        self.client = WOQLClient(server_url=server_url)
-        self.client.connect(user=user, key=key, account=account)
-        db_info = self.client.get_database(dbid=dbid, account=account)
-        if db_info is None:
-            self.client.create_database(dbid=dbid, accountid=account, label=dbid)
-            self.client.create_graph(graph_type="inference", graph_id="main")
-        self.client.connect(user=user, key=key, account=account, db=dbid)
-
-
-@resource(
-    config_schema={
-        "server_url": StringSource,
-        "user": StringSource,
-        "key": StringSource,
-        "account": StringSource,
-        "dbid": StringSource,
-    }
-)
-def terminus_resource(context):
-    return TerminusDB(
-        server_url=context.resource_config["server_url"],
-        user=context.resource_config["user"],
-        key=context.resource_config["key"],
-        account=context.resource_config["account"],
-        dbid=context.resource_config["dbid"],
-    )