Merge branch 'main' into readme

Author: davidsklar99

.env.sample

@@ -0,0 +1,2 @@
+schema=<schema>
+uri=<uri>

.github/workflows/image.yaml

@@ -15,4 +15,4 @@ jobs:
     with:
       image: 'hub.opensciencegrid.org/macrostrat/macrostrat-xdd'
       context: macrostrat_db_insertion
-      file: macrostrat_db_insertion/Dockerfile
+      file: macrostrat_db_insertion/Dockerfile

README.md

@@ -56,18 +56,15 @@ The API endpoint is a Flask server that uses SQLAlchemy to verify the input data
 The code for the server can be found in the `macrostrat_db_insertion` directory. We have provided a docker container that contains all of the necessary dependencies which you can setup using:
 ```
 $ cd macrostrat_db_insertion
-$ export CURRENT_DIR=`pwd`
-$ docker build -t db_insert:latest .
-$ docker run -d -v $CURRENT_DIR:/working_dir/ --name=db_insert --entrypoint /bin/bash -p 9543:9543 db_insert:latest -c "sleep infinity"
-$ docker exec -it db_insert bash
+$ make build
 $ conda activate db_insert_env
 $ pkill -9 -f "server"
 $ export PYTHONPATH="${PYTHONPATH}:/working_dir"
 ```
 
 Then you can launch the server using:
 ```
-$ python3 -u server.py &> server_requests.log &
+$ python3 -u -m macrostrat_db_insertion.server &> server_requests.log &
 ```
 
 which will launch the server on port `9543` as a background process. Note that to properly launch the server, the environment variables `uri`, and `schema` must be set to the proper values so that the server can properly communicate

macrostrat_db_insertion/Dockerfile

@@ -20,6 +20,10 @@ RUN source ~/.bashrc
 
 WORKDIR /app
 
+# Accept conda terms of service
+RUN conda tos accept --override-channels --channel https://repo.anaconda.com/pkgs/main && \
+    conda tos accept --override-channels --channel https://repo.anaconda.com/pkgs/r
+
 # Create and activate conda environment
 COPY environment.yml environment.yml
 RUN conda env create -f environment.yml

macrostrat_db_insertion/Makefile

@@ -0,0 +1,13 @@
+build:
+	@export CURRENT_DIR=$$(pwd); \
+	docker rm -f db_insert 2>/dev/null || true; \
+	docker build -t db_insert:latest .; \
+	docker run -d \
+		-v $$CURRENT_DIR:/working_dir/ \
+		--env-file $$CURRENT_DIR/.env \
+		--name=db_insert \
+		--entrypoint /bin/bash \
+		-p 9543:9543 \
+		db_insert:latest \
+		-c "sleep infinity"; \
+	docker exec -it db_insert bash

macrostrat_db_insertion/server.py

@@ -921,7 +921,7 @@ def process_user_feedback_input_request(request_data, session):
             if not success:
                 return success, err_msg
 
-    return True, None
+    return True, request_additional_data["internal_run_id"]
 
 # Opentially take in user id
 @app.post("/record_run")
@@ -931,7 +931,6 @@ async def record_run(
         user_id: str | None = Depends(get_user_id),
         session: Session = Depends(get_session)
 ):
-
     if not user_has_access:
         raise HTTPException(status_code=403, detail="User does not have access to record run")
 
@@ -952,8 +951,14 @@ async def record_run(
         print("Returning error message", error_msg)
         raise HTTPException(status_code=400, detail=error_msg)
 
-    return JSONResponse(content={"success": "Successfully processed the run"})
+    table_id = error_msg
 
+    return JSONResponse(content={
+        "success": "Successfully processed the run",
+        "data": {
+            "table_id": str(table_id)
+        }
+    })
 
 @app.get("/health")
 async def health(