More small fixes

Dockerfile

@@ -2,14 +2,15 @@ FROM rstudio/plumber:latest
 
 ENV TZ "Africa/Nairobi"
 
-RUN apt-get -y update && apt-get -y install \
+RUN apt-get -y update -qq && apt-get -y --no-install-recommends install \
 	tini \
 	libmariadb-dev \
 	libmysqlclient21 \
 	openjdk-8-jdk-headless \
 	cron \
 	curl \
-	&& rm -rf /var/lib/apt/lists/*
+	&& rm -rf /var/lib/apt/lists/* \
+	&& rm -rf /etc/cron.*/*
 
 RUN install2.r --error --skipinstalled \
 	tidyverse \
@@ -24,23 +25,25 @@ RUN install2.r --error --skipinstalled \
 
 RUN Rscript -e "remotes::install_version('h2o', '3.42.0.2')"
 
-COPY docker-resources/crontab /etc/cron.d/iit-crontab
 COPY IIT-Prediction/model/V7 /app/model
 COPY SQL/iit_prod_data_extract.sql /app/iit_prod_data_extract.sql
 COPY docker-resources/run_predictions.sh /app/run_predictions.sh
 RUN chmod 0744 /app/run_predictions.sh
 COPY docker-resources/run_daily_stored_procedures.sh /app/run_daily_stored_procedures.sh
 RUN chmod 0744 /app/run_daily_stored_procedures.sh
-COPY docker-resources/dailyStoredProcedures.R /app/dailyStoredProcedures.R
 COPY docker-resources/docker-entrypoint.sh /docker-entrypoint.sh
 RUN chmod 0744 /docker-entrypoint.sh
-COPY docker-resources/plumber.R /app/plumber.R
+
+COPY docker-resources/crontab /etc/cron.d/iit-crontab
 RUN chmod 0644 /etc/cron.d/iit-crontab
-RUN crontab /etc/cron.d/iit-crontab
+RUN crontab -u root /etc/cron.d/iit-crontab
 RUN touch /var/log/cron.log
 
+COPY docker-resources/dailyStoredProcedures.R /app/dailyStoredProcedures.R
+COPY docker-resources/plumber.R /app/plumber.R
+
 EXPOSE 8000
 
-ENTRYPOINT ["tini", "--", "./docker-entrypoint.sh"]
+ENTRYPOINT ["tini", "--", "/docker-entrypoint.sh"]
 
 CMD ["/app/plumber.R"]

docker-resources/dailyStoredProcedures.R

@@ -32,3 +32,5 @@ DBI::dbExecute(
   my_pool,
   "CALL predictions.add_observed_appointments_to_ml_predictions_v1_0();"
 )
+
+poolClose(my_pool)

docker-resources/plumber.R

@@ -34,6 +34,8 @@ my_pool <- dbPool(
   dbname = dbConfig$defaultDb
 )
 
+on.exit(poolClose(my_pool))
+
 # Custom router modifications
 #* @plumber
 function(pr) {
@@ -136,6 +138,7 @@ function(
   prediction_results_adults <- predictors %>%
     filter(Age >= 18) %>%
     bind_cols(as.data.frame(results_adults)) %>%
+    left_join(results_adults, by = join_by(person_id, encounter_id, location_id)) %>%
     # reduce data frame and rename the result
     select(person_id, encounter_id, location_id, rtc_date, predicted_prob_disengage = Disengaged) %>%
     # calculate the patient's risk category
@@ -153,6 +156,7 @@ function(
   prediction_results_minors <- predictors %>%
     filter(Age < 18) %>%
     bind_cols(as.data.frame(results_minors)) %>%
+    left_join(results_minors, by = join_by(person_id, encounter_id, location_id)) %>%
     # reduce data frame and rename the result
     select(person_id, encounter_id, location_id, rtc_date, predicted_prob_disengage = Disengaged) %>%
     # calculate the patient's risk category