From 2880c08742d75ceaa02ce2567ba24b7ff0c47f8d Mon Sep 17 00:00:00 2001
From: Milan Malfait <38256462+milanmlft@users.noreply.github.com>
Date: Wed, 20 Nov 2024 18:35:56 +0100
Subject: [PATCH] Simplify: use `SUMMARISE_LEVEL` envvar only in preprocessing

Just rely on column name in app
---
 .env.sample        | 16 +++++++---------
 docker-compose.yml |  3 +--
 public.env.sample  | 16 +++++++---------
 3 files changed, 15 insertions(+), 20 deletions(-)

diff --git a/.env.sample b/.env.sample
index 2c2a79f..cb708a9 100644
--- a/.env.sample
+++ b/.env.sample
@@ -4,19 +4,17 @@ DATA_VOLUME_PATH=./data/test_data/internal
 SHINY_PORT: 3838
 
 # For preprocessing
-PREPROCESS_DB_NAME=         # name of the source database
-PREPROCESS_HOST=            # host address for the source database
-PREPROCESS_PORT=            # port on which to connect to the source database
-PREPROCESS_DB_USERNAME=     # username for the source database
-PREPROCESS_DB_PASSWORD=     # password for the source database
-PREPROCESS_DB_CDM_SCHEMA=   # Schema name in the database to connect the OMOP CDM to 
+PREPROCESS_DB_NAME=                 # name of the source database
+PREPROCESS_HOST=                    # host address for the source database
+PREPROCESS_PORT=                    # port on which to connect to the source database
+PREPROCESS_DB_USERNAME=             # username for the source database
+PREPROCESS_DB_PASSWORD=             # password for the source database
+PREPROCESS_DB_CDM_SCHEMA=           # Schema name in the database to connect the OMOP CDM to
+PREPROCESS_SUMMARISE_LEVEL=monthly  # Level to summarise record counts at (monthly or quarterly)
 
 # Low-frequency replacement
 LOW_FREQUENCY_THRESHOLD=5
 LOW_FREQUENCY_REPLACEMENT=2.5
 
-# Level to summarise record counts at (monthly or quarterly)
-SUMMARISE_LEVEL=monthly
-
 # For testing
 TEST_DB_PATH=./data-raw/test_db/eunomia
diff --git a/docker-compose.yml b/docker-compose.yml
index 27a04b9..2bc2a52 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -21,7 +21,7 @@ services:
       EUNOMIA_DATA_FOLDER: /mnt/preprocessing/data-raw/test_db
       LOW_FREQUENCY_THRESHOLD: ${LOW_FREQUENCY_THRESHOLD}
       LOW_FREQUENCY_REPLACEMENT: ${LOW_FREQUENCY_REPLACEMENT}
-      SUMMARISE_LEVEL: ${SUMMARISE_LEVEL}
+      SUMMARISE_LEVEL: ${PREPROCESS_SUMMARISE_LEVEL}
     command: ["R", "-e", "omopcat.preprocessing::preprocess()"]
     volumes:
       - ${DATA_VOLUME_PATH}:/mnt/preprocessing/data
@@ -47,7 +47,6 @@ services:
       OMOPCAT_DATA_PATH: /etc/omopcat/data
       LOW_FREQUENCY_THRESHOLD: ${LOW_FREQUENCY_THRESHOLD}
       LOW_FREQUENCY_REPLACEMENT: ${LOW_FREQUENCY_REPLACEMENT}
-      SUMMARISE_LEVEL: ${SUMMARISE_LEVEL}
     volumes:
       - ${DATA_VOLUME_PATH}:/etc/omopcat/data
     ports:
diff --git a/public.env.sample b/public.env.sample
index b388180..1378e1d 100644
--- a/public.env.sample
+++ b/public.env.sample
@@ -4,19 +4,17 @@ DATA_VOLUME_PATH=./data/test_data/public
 SHINY_PORT: 3839
 
 # For preprocessing
-PREPROCESS_DB_NAME=         # name of the source database
-PREPROCESS_HOST=            # host address for the source database
-PREPROCESS_PORT=            # port on which to connect to the source database
-PREPROCESS_DB_USERNAME=     # username for the source database
-PREPROCESS_DB_PASSWORD=     # password for the source database
-PREPROCESS_DB_CDM_SCHEMA=   # Schema name in the database to connect the OMOP CDM to 
+PREPROCESS_DB_NAME=                 # name of the source database
+PREPROCESS_HOST=                    # host address for the source database
+PREPROCESS_PORT=                    # port on which to connect to the source database
+PREPROCESS_DB_USERNAME=             # username for the source database
+PREPROCESS_DB_PASSWORD=             # password for the source database
+PREPROCESS_DB_CDM_SCHEMA=           # Schema name in the database to connect the OMOP CDM to
+PREPROCESS_SUMMARISE_LEVEL=quarterly  # Level to summarise record counts at (monthly or quarterly)
 
 # Low-frequency replacement
 LOW_FREQUENCY_THRESHOLD=10
 LOW_FREQUENCY_REPLACEMENT=5
 
-# Level to summarise record counts at (monthly or quarterly)
-SUMMARISE_LEVEL=quarterly
-
 # For testing
 TEST_DB_PATH=./data-raw/test_db/eunomia