Implemented minor changes

docker/hapi-compose.yml

@@ -32,8 +32,6 @@ services:
     container_name: hapi-server
     environment:
       - hapi.fhir.mdm_enabled=false
-      - hapi.fhir.enforce_referential_integrity_on_delete=false
-      - hapi.fhir.enforce_referential_integrity_on_write=false
       - spring.datasource.url=jdbc:postgresql://db:5432/hapi
       - spring.datasource.username=admin
       - spring.datasource.password=admin
@@ -43,9 +41,7 @@ services:
     restart: unless-stopped
     ports:
       - 8098:8080
-    volumes:
-      - hapi-server:/data/hapi
-
+
 volumes:
   hapi-fhir-db:
   hapi-server:

utils/resource-monitor/README.md

@@ -1,8 +1,8 @@
 # Resource performance monitoring and graphing module
 
-This is a module for monitoring the resource usage of the batch pipeline with [HAPI](https://hapifhir.io/) 
+This is a module for monitoring the resource usage of the batch pipeline with [HAPI FHIR](https://hapifhir.io/) 
 as the source. The scripts in this module generate graphs and csv files of resource usage 
-(CPU, memory and I/O) of the HAPI server, postgres database and pipeline over the duration of the 
+(CPU, memory and I/O) of the HAPI server, PostgreSQL database and pipeline over the duration of the 
 batch job. The user is able to specify the number of processes/cores used in the pipeline to assess 
 the batch pipeline's performance on the local machine.
 
@@ -11,11 +11,12 @@ the batch pipeline's performance on the local machine.
 -   Ensure you are able to run the `docker` command 
 [as a non-root user](https://docs.docker.com/engine/install/linux-postinstall/). If not, run  
 `sudo chmod 666 /var/run/docker.sock`
--   A [HAPI](https://hapifhir.io/) instance with a [postgres](https://www.postgresql.org/) instance 
-as its database. For convenience, [`this`](/docker/hapi-compose.yml) .yml file in the in the 
+-   A [HAPI](https://hapifhir.io/) instance with a [PostgreSQL](https://www.postgresql.org/) instance 
+as its database. For convenience, [`hapi-compose.yml`](/docker/hapi-compose.yml) file in the in the 
 [`docker`](/docker) directory contains images of a HAPI server using postrges as its database. Start 
 the docker container with  
-`docker-compose -f hapi-compose.yml up` 
+`docker-compose -f hapi-compose.yml up`
+-   To upload sample data in the HAPI sever, please refer to this [`document`](/synthea-hiv/README.md).
 
 ## Graphing module
 
@@ -37,7 +38,7 @@ python3 graph_pidstat.py \
 
 The output graphs can be found in the output results directory specified by the user; 
 the default is `/tmp/hapi-performance/`. The graphs visualize the CPU, memory and I/O usage of the 
-HAPI server, postgres database and pipeline over the duration of the batch job.
+HAPI server, PostgreSQL database and pipeline over the duration of the batch job.
 
 ## Automating runs with different number of cores
 

utils/resource-monitor/auto.sh

@@ -16,7 +16,7 @@ if [[ "$#" -ne 6 ]]; then
     printf '%s\n' \
         "Error: Illegal number of arguments. " \
         "Example usage: " \
-        "sh auto.sh [data description] [output parquet path] [output results path] [num processes increment] [lower core limit] [upper core limit]"
+        "sh $0 [data description] [output parquet path] [output results path] [num processes increment] [lower core limit] [upper core limit]"
     exit 1
 fi
 

utils/resource-monitor/graph_pidstat.py

@@ -74,7 +74,7 @@ def get_machine_mem() -> int:
       None
 
     Returns:
-      Integer representation of the local machine RAM in MBs
+      Integer representation of the local machine RAM in GBs
     """
     mem_info = subprocess.run(
         ["grep", "MemTotal", "/proc/meminfo"], stdout=subprocess.PIPE