Various retrospective improvements

Dockerfile

@@ -1,6 +1,6 @@
 FROM rstudio/plumber:latest
 
-ENV TZ "Africa/Nairobi"
+ENV TZ="Africa/Nairobi"
 
 # install base libraries we need
 RUN apt-get -y update -qq && apt-get -y --no-install-recommends install \

SQL/iit_prod_data_extract.sql

@@ -149,4 +149,4 @@ where
   -- filter dead patients
   and fs.death_date is null
   -- if not run retrospectively, don't generate new predictions for existing cases
-  and (?retrospective or mlp.encounter_id is null);
+  and (?retrospectiveTest or mlp.encounter_id is null);

docker-resources/plumber.R

@@ -89,14 +89,22 @@ cors <- function(req, res) {
 #* @serializer json
 #* @post /predict
 function(
-  startDate = NA,       # the startDate is the first day to start from
-                        # note that it will be adjusted to the Monday of the week its in as we always run in weekly batches
-  weeks = "1",          # the number of weeks to run; this is only used for testing
-  retrospective = "F"   # whether or not the query is retrospective (run against past data for testing) or prospective
-                        # (run normally); this mostly adjusts the query
+  startDate = NA,           # the startDate is the first day to start from
+                            # note that it will be adjusted to the Monday of the week its in as we always run in weekly batches
+  weeks = "1",              # the number of weeks to run; this is only used for testing
+  retrospective = "F",      # whether or not the query is retrospective (run against past data for testing) or prospective
+                            # (run normally); this mostly adjusts the query
+  retrospectiveTest = NA    # whether, when run retrospectively, to treat the run as a "test", so to generate all results
+                            # and not write to the predictions table
 ) {
   retrospective <- as.logical(retrospective)
 
+  if (is.na(retrospectiveTest)) {
+    retrospectiveTest = retrospective
+  } else {
+    retrospectiveTest = as.logical(retrospectiveTest)
+  }
+
   # If the startDate is not specified, it defaults to NA and we set it to a week from today
   if (is.na(startDate)) {
     startDate = clock::add_weeks(Sys.Date(), 1)
@@ -119,7 +127,8 @@ function(
     ml_sql,
     startDate = start_of_week,
     endDate = end_of_week,
-    retrospective = retrospective
+    retrospective = retrospective,
+    retrospectiveTest = retrospectiveTest
   )
 
   # run the query, giving us a dataframe
@@ -217,7 +226,9 @@ function(
   prediction_result <- bind_rows(prediction_results_adults, prediction_results_minors)
 
   # add the rows from the prediction_result to the ml_weekly_predictions table
-  DBI::dbAppendTable(my_pool, SQL('predictions.ml_weekly_predictions'), prediction_result)
+  if (!retrospectiveTest) {
+    DBI::dbAppendTable(my_pool, SQL('predictions.ml_weekly_predictions'), prediction_result)
+  }
 
   # return the result so the API returns *something*
   prediction_result