Count the instance_num when pushing observations

R/demodata.R

@@ -262,16 +262,6 @@ add_patients_demodata <- function(patients, project, host = "", admin = "", pass
 {
   demodata <- RPostgreSQL::dbConnect(RPostgreSQL::PostgreSQL(), host = host, dbname = stringr::str_c("i2b2", stringr::str_to_lower(project), "data"), user = admin, password = pass)
 
-# Upsert patients mappings
-  # patients %>%
-  #   dplyr::mutate(patient_ide_source = "HIVE",
-  #                 patient_ide_status = "A",
-  #                 project_id = project,
-  #                 patient_num = patient_ide,
-  #                 update_date = format(Sys.Date(), "%m/%d/%Y")) %>%
-  #   dplyr::select(patient_ide, patient_ide_source, patient_num, patient_ide_status, project_id, update_date) %>%
-  # dbUpsert(demodata, "patient_mapping", c("patient_ide", "patient_ide_source", "project_id"))
-
 # Upsert patients mappings
   patients %>%
     dplyr::mutate(patient_ide_source = project,
@@ -319,7 +309,6 @@ add_encounters <- function(encounters, project, host = "", admin = "", pass = ""
 
   demodata %>%
     dplyr::tbl("encounter_mapping") %>%
-    # dplyr::filter(encounter_ide_source == "HIVE") %>%
     dplyr::select(encounter_ide, encounter_num) %>%
     dplyr::collect() ->
   mapping
@@ -336,15 +325,6 @@ add_encounters <- function(encounters, project, host = "", admin = "", pass = ""
     dplyr::anti_join(mapping) %>%
     dplyr::mutate(encounter_num = seq(start, length.out = nrow(.))) -> unmapped
 
-  # unmapped %>%
-  #     dplyr::mutate(encounter_ide_source = "HIVE",
-  #                   encounter_ide_status  = "A",
-  #                   project_id = project,
-  #                   patient_ide_source = "HIVE",
-  #                   update_date = format(Sys.Date(), "%m/%d/%Y")) %>%
-  #     dplyr::select(encounter_ide, encounter_ide_source, project_id, encounter_num, patient_ide, patient_ide_source, encounter_ide_status, update_date) %>%
-  # dbUpsert(demodata, "encounter_mapping", c("encounter_ide", "encounter_ide_source", "project_id", "patient_ide", "patient_ide_source"))
-
   unmapped %>%
       dplyr::mutate(encounter_ide_source = project,
                     encounter_ide_status  = "A",
@@ -395,9 +375,9 @@ add_observations <- function(observations, project, host = "", admin = "", pass
 {
   demodata <- RPostgreSQL::dbConnect(RPostgreSQL::PostgreSQL(), host = host, dbname = stringr::str_c("i2b2", stringr::str_to_lower(project), "data"), user = admin, password = pass)
 
+  # Get the encounter mapping
   demodata %>%
     dplyr::tbl("encounter_mapping") %>%
-    # dplyr::filter(encounter_ide_source == "HIVE") %>%
     dplyr::select(encounter_ide, encounter_num) %>%
     dplyr::collect() ->
   mapping
@@ -405,6 +385,7 @@ add_observations <- function(observations, project, host = "", admin = "", pass
   observations %>%
     dplyr::inner_join(mapping) -> observations
 
+  # create the text_search_index column
   RPostgreSQL::dbGetQuery(demodata, "SELECT max(text_search_index) from observation_fact;") %>%
   .$max -> nextval
 
@@ -419,6 +400,9 @@ add_observations <- function(observations, project, host = "", admin = "", pass
                   patient_num = patient_ide,
                   update_date = format(Sys.Date(), "%m/%d/%Y"),
                   text_search_index = seq(nextval+1, length.out = nrow(.))) %>%
+    dplyr::group_by(patient_ide, encounter_ide, start_date, provider_id, concept_cd, modifier_cd) %>%
+    dplyr::mutate(instance_num = seq(1, length.out = n())) %>%
+    dplyr::ungroup() %>%
     dplyr::select(-patient_ide, -encounter_ide) %>%
   dbUpsert(demodata, "observation_fact", c("patient_num", "concept_cd", "modifier_cd", "start_date", "encounter_num", "instance_num", "provider_id"))