Set low-freq replacement envvars in docker context

SAFEHR-data · Nov 15, 2024 · 3f69af0 · 3f69af0
1 parent c89f00c
commit 3f69af0
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Showing 2 changed files with 8 additions and 2 deletions.
diff --git a/.env.sample b/.env.sample
@@ -8,5 +8,9 @@ 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
 
+# Low-frequency replacement
+LOW_FREQUENCY_THRESHOLD=5
+LOW_FREQUENCY_REPLACEMENT=2.5
+
 # For testing
 TEST_DB_PATH=./data-raw/test_db/eunomia
diff --git a/docker-compose.yml b/docker-compose.yml
@@ -19,6 +19,8 @@ services:
       DB_PASSWORD: ${PREPROCESS_DB_PASSWORD}
       DB_CDM_SCHEMA: ${PREPROCESS_DB_CDM_SCHEMA}
       EUNOMIA_DATA_FOLDER: /mnt/preprocessing/data-raw/test_db
+      LOW_FREQUENCY_THRESHOLD: ${LOW_FREQUENCY_THRESHOLD}
+      LOW_FREQUENCY_REPLACEMENT: ${LOW_FREQUENCY_REPLACEMENT}
     command: ["R", "-e", "omopcat.preprocessing::preprocess()"]
     volumes:
       - ${DATA_VOLUME_PATH}:/mnt/preprocessing/data
@@ -42,8 +44,8 @@ services:
       HTTPS_PROXY: ${HTTPS_PROXY}
       GOLEM_CONFIG_ACTIVE: production
       OMOPCAT_DATA_PATH: /etc/omopcat/data
-      LOW_FREQUENCY_THRESHOLD: 5
-      LOW_FREQUENCY_REPLACEMENT: 2.5
+      LOW_FREQUENCY_THRESHOLD: ${LOW_FREQUENCY_THRESHOLD}
+      LOW_FREQUENCY_REPLACEMENT: ${LOW_FREQUENCY_REPLACEMENT}
     volumes:
       - ${DATA_VOLUME_PATH}:/etc/omopcat/data
     ports: