Initial data portal endpoints

.gitignore

@@ -160,4 +160,7 @@ repl.ipynb
 
 tests/nmdcdb/
 
-neon_cache.sqlite
+neon_cache.sqlite
+
+# output of changesheet generation
+nmdc_runtime/site/changesheets/changesheets_output/

README.md

@@ -6,8 +6,8 @@ http://nmdcstatus.polyneme.xyz/
 
 ## How It Fits In
 
-* [nmdc-metadata](https://github.com/microbiomedata/nmdc-metadata)
-tracks issues related to NMDC metadata, which may necessitate work across multiple repos.
+* [issues](https://github.com/microbiomedata/issues)  
+tracks issues related to NMDC, which may necessitate work across multiple repos.
 
 * [nmdc-schema](https://github.com/microbiomedata/nmdc-schema/)
 houses the LinkML schema specification, as well as generated artifacts (e.g. JSON Schema).
@@ -111,7 +111,7 @@ If you are connecting to resources that require an SSH tunnel—for example, a M
 The following command could be useful to you, either directly or as a template (see `Makefile`).
 
 ```shell
-make nersc-ssh-tunnel
+make nersc-mongo-tunnels
 ```
 
 Finally, spin up the Docker Compose stack.

components/nmdc_runtime/workflow_execution_activity/core.py

@@ -94,7 +94,9 @@ def insert_into_keys(
     workflow: Workflow, data_objects: list[DataObject]
 ) -> dict[str, Any]:
     """Insert data object url into correct workflow input field."""
-    workflow_dict = workflow.dict()
+    workflow_dict = workflow.model_dump(
+        mode="json",
+    )
     for key in workflow_dict["inputs"]:
         for do in data_objects:
             if workflow_dict["inputs"][key] == str(do.data_object_type):

components/nmdc_runtime/workflow_execution_activity/spec.py

@@ -6,10 +6,11 @@
     WorkflowExecutionActivity,
     Database,
 )
-from pydantic import BaseModel
+from pydantic import BaseModel, ConfigDict
 
 
 class ActivityTree(BaseModel):
+    model_config = ConfigDict(arbitrary_types_allowed=True)
     children: list["ActivityTree"] = []
     data: WorkflowExecutionActivity
     spec: Workflow

docker-compose.test.yml

@@ -36,6 +36,7 @@ services:
       DAGSTER_POSTGRES_DB: "postgres_db"
     depends_on:
       - dagster-postgresql
+    restart: on-failure
     volumes:
       - ./:/opt/dagster/lib
 

docker-compose.yml

@@ -36,6 +36,7 @@ services:
       DAGSTER_POSTGRES_DB: "postgres_db"
     depends_on:
       - dagster-postgresql
+    restart: on-failure
     volumes:
       - ./:/opt/dagster/lib
 

docs/nb/get_data.ipynb

@@ -640,8 +640,7 @@
       "32,590.4511390833583,590.450730484585,,33051017.328779608,174529.72008540362,95.62528562170476,-1,,,,,,,,unassigned,,,,,,,,,\n",
       "33,574.4557295997837,574.4553249571502,,57270445.86539885,179389.47009937343,165.6984621406013,-1,,,,,,,,unassigned,,,,,,,,,\n",
       "34,509.29372586837684,509.2933397523243,,3016102.9919072534,115624.41149005273,8.726379197243881,-1,,,,,,,,unassigned,,,,,,,,,\n",
-      "36,311.1007284631918,311.10042248349583,,2602658.391103224,220831.98006834995,7.530175230287296,-1,,,,,,,,unassigned,,,,,,,,,\n",
-      "\n"
+      "36,311.1007284631918,311.10042248349583,,2602658.391103224,220831.98006834995,7.530175230287296,-1,,,,,,,,unassigned,,,,,,,,,\n"
      ]
     }
    ],

nmdc_runtime/api/core/auth.py

@@ -35,7 +35,7 @@ class TokenExpires(BaseModel):
 class Token(BaseModel):
     access_token: str
     token_type: str
-    expires: Optional[TokenExpires]
+    expires: Optional[TokenExpires] = None
 
 
 class TokenData(BaseModel):
@@ -95,8 +95,25 @@ def __init__(
         super().__init__(flows=flows, scheme_name=scheme_name, auto_error=auto_error)
 
     async def __call__(self, request: Request) -> Optional[str]:
-        authorization: str = request.headers.get("Authorization")
-        scheme, param = get_authorization_scheme_param(authorization)
+        header_authorization: str = request.headers.get("Authorization")
+        cookie_authorization: str = f"Bearer {request.cookies.get('session')}"
+        header_scheme, header_param = get_authorization_scheme_param(
+            header_authorization
+        )
+        cookie_scheme, cookie_param = get_authorization_scheme_param(
+            cookie_authorization
+        )
+        scheme, param = "", ""
+        if header_scheme.lower() == "bearer":
+            authorization = True
+            scheme = header_scheme
+            param = header_param
+        elif cookie_scheme.lower() == "bearer":
+            authorization = True
+            scheme = cookie_scheme
+            param = cookie_param
+        else:
+            authorization = False
         if not authorization or scheme.lower() != "bearer":
             if self.auto_error:
                 raise HTTPException(

nmdc_runtime/api/core/util.py

@@ -98,6 +98,6 @@ def generate_secret(length=12):
 def json_clean(data, model, exclude_unset=False) -> dict:
     """Run data through a JSON serializer for a pydantic model."""
     if not isinstance(data, (dict, BaseModel)):
-        raise TypeError("`data` must be a pydantic model or its .dict()")
+        raise TypeError("`data` must be a pydantic model or its .model_dump()")
     m = model(**data) if isinstance(data, dict) else data
     return json.loads(m.json(exclude_unset=exclude_unset))

nmdc_runtime/api/endpoints/find.py

@@ -266,7 +266,7 @@ def pipeline_search(
     response_model=PipelineFindResponse,
     response_model_exclude_unset=True,
 )
-def pipeline_search(
+def pipeline_search_form(
     pipeline_spec: str = Form(...),
     description: str = Form(...),
     mdb: MongoDatabase = Depends(get_mongo_db),
@@ -276,7 +276,7 @@ def pipeline_search(
 
 
 @router.get("/pipeline_search", response_class=HTMLResponse)
-def pipeline_search(
+def pipeline_search_get(
     mdb: MongoDatabase = Depends(get_mongo_db),
 ):
     template = jinja_env.get_template("pipeline_search.html")

nmdc_runtime/api/endpoints/objects.py

@@ -78,7 +78,7 @@ def create_object(
 
     """
     id_supplied = supplied_object_id(
-        mdb, client_site, object_in.dict(exclude_unset=True)
+        mdb, client_site, object_in.model_dump(mode="json", exclude_unset=True)
     )
     drs_id = local_part(
         id_supplied if id_supplied is not None else generate_one_id(mdb, S3_ID_NS)
@@ -255,7 +255,9 @@ def update_object(
             status_code=status.HTTP_403_FORBIDDEN,
             detail=f"client authorized for different site_id than {object_mgr_site}",
         )
-    doc_object_patched = merge(doc, object_patch.dict(exclude_unset=True))
+    doc_object_patched = merge(
+        doc, object_patch.model_dump(mode="json", exclude_unset=True)
+    )
     mdb.operations.replace_one({"id": object_id}, doc_object_patched)
     return doc_object_patched
 

nmdc_runtime/api/endpoints/operations.py

@@ -61,12 +61,16 @@ def update_operation(
             detail=f"client authorized for different site_id than {site_id_op}",
         )
     op_patch_metadata = merge(
-        op_patch.dict(exclude_unset=True).get("metadata", {}),
+        op_patch.model_dump(mode="json", exclude_unset=True).get("metadata", {}),
         pick(["site_id", "job", "model"], doc_op.get("metadata", {})),
     )
     doc_op_patched = merge(
         doc_op,
-        assoc(op_patch.dict(exclude_unset=True), "metadata", op_patch_metadata),
+        assoc(
+            op_patch.model_dump(mode="json", exclude_unset=True),
+            "metadata",
+            op_patch_metadata,
+        ),
     )
     mdb.operations.replace_one({"id": op_id}, doc_op_patched)
     return doc_op_patched