Import data functions

R/import.R

@@ -1,47 +1,125 @@
-#' Import data into i2b2
-#'
-#' Import data from a data frame into i2b2
-#'
-#' The data dataframe must contain the following columns:
-#' - encounter_ide: the original encounter ID
-#' - patient_ide: the original patient ID
-#' - start_date: the start date of the encounter, as Date object
-#' - concept_cd: the concept to insert
-#' - provider_id: the provider
-#' - modifier_cd: optionnal modifier for the concept
-#' Other observation fact columns can optionnaly be included,
-#' such as end_date, valtype_cd, tval_char, nval_num, valueflag_cd, units_cd, etc.
-#'
-#' The function creates and updates the corresponding patients and encounters,
-#' inserts the new observations, and finally rebuilds the indexes in the database.
-#'
-#' @param data A dataframe of observation facts
-#' @param project The project to which to add the patients and their data
-#' @param host The host to connect to
-#' @param admin The admin account for the PostgreSQL database
-#' @param pass The password for the admin account
-#' @export
-import_data <- function(data, project, host = "", admin = "", pass = "")
+# #' Import data into i2b2
+# #'
+# #' Import data from a data frame into i2b2
+# #'
+# #' The data dataframe must contain the following columns:
+# #' - encounter_ide: the original encounter ID
+# #' - patient_ide: the original patient ID
+# #' - start_date: the start date of the encounter, as Date object
+# #' - concept_cd: the concept to insert
+# #' - provider_id: the provider
+# #' - modifier_cd: optionnal modifier for the concept
+# #' Other observation fact columns can optionnaly be included,
+# #' such as end_date, valtype_cd, tval_char, nval_num, valueflag_cd, units_cd, etc.
+# #'
+# #' The function creates and updates the corresponding patients and encounters,
+# #' inserts the new observations, and finally rebuilds the indexes in the database.
+# #'
+# #' @param data A dataframe of observation facts
+# #' @param project The project to which to add the patients and their data
+# #' @param host The host to connect to
+# #' @param admin The admin account for the PostgreSQL database
+# #' @param pass The password for the admin account
+# #' @export
+# import_data <- function(data, project, host = "", admin = "", pass = "")
+# {
+#   # Patients
+#   data %>%
+#     dplyr::select(patient_ide, birth_date, death_date, gender) %>%
+#     dplyr::distinct() %>%
+#     add_patients_demodata(project, host, admin, pass) ->
+#   patient_mapping
+
+#   # Encounters
+#   data %>%
+#     dplyr::select(patient_ide, encounter_ide, start_date, end_date) %>%
+#     dplyr::distinct() %>%
+#     add_encounters(project, patient_mapping, host, admin, pass) ->
+#   encounter_mapping
+
+#   # Observations
+#   data %>%
+#     dplyr::distinct() %>%
+#   add_observations(patient_mapping, encounter_mapping, host, admin, pass)
+
+#   # Rebuild indexes
+#   rebuild_indexes_demodata(host, admin, pass)
+# }
+
+import_patients_visits <- function(patients, project)
 {
+  patients %>%
+    stats::setNames(c("patient_ide", "encounter_ide", "start_date", "end_date", "sex_cd", "birth_date", "death_date", "rum_start", "rum_end", "provider_id", "project")) %>%
+    dplyr::mutate(start_date = start_date %>% as.Date(format = "%Y/%m/%d %H:%M:%S"),
+           end_date = end_date %>% as.Date(format = "%Y/%m/%d %H:%M:%S"),
+           birth_date = birth_date %>% as.Date(format = "%Y/%m/%d %H:%M:%S"),
+           death_date = death_date %>% as.Date(format = "%Y/%m/%d %H:%M:%S"),
+           sex_cd = ifelse(sex_cd == "1", "M", "F")) %>%
+    dplyr::filter(!is.na(patient_ide)) %>%
+    dplyr::mutate(patient_ide = ifelse(patient_ide %>% as.numeric > 2^32,
+                                patient_ide %>% stringr::str_sub(2),
+                                patient_ide)) ->
+  patients
+
   # Patients
-  data %>%
-    dplyr::select(patient_ide, birth_date, death_date, gender) %>%
+  patients %>%
+    dplyr::select(patient_ide, birth_date, death_date, sex_cd) %>%
     dplyr::distinct() %>%
-    add_patients_demodata(project, host, admin, pass) ->
-  patient_mapping
+    add_patients_demodata(project)
 
   # Encounters
-  data %>%
+  patients %>%
     dplyr::select(patient_ide, encounter_ide, start_date, end_date) %>%
     dplyr::distinct() %>%
-    add_encounters(project, patient_mapping, host, admin, pass) ->
-  encounter_mapping
+    dplyr::mutate(inout = "I") %>%
+    add_encounters(project)
 
-  # Observations
-  data %>%
+  # Observations : Age à l'hospitalisation
+  patients %>%
+    dplyr::select(patient_ide, encounter_ide, start_date, birth_date, provider_id) %>%
     dplyr::distinct() %>%
-  add_observations(patient_mapping, encounter_mapping, host, admin, pass)
+    dplyr::mutate(concept_cd = "HOS:age_hospit",
+           provider_id = stringr::str_c("STRUCT:", provider_id),
+           modifier_cd = "@",
+           instance_num = 1,
+           valtype_cd = "N",
+           tval_char = "E",
+           nval_num = as.numeric(start_date - birth_date)/365.25) %>%
+    dplyr::select(-birth_date) %>%
+    add_observations(project)
+}
 
-  # Rebuild indexes
-  rebuild_indexes_demodata(host, admin, pass)
+import_diagnostics <- function(diags, project)
+{
+  # Observations : Diagnostics
+  diags %>%
+    stats::setNames(c("patient_ide", "encounter_ide", "start_date", "end_date", "provider_id", "concept_cd", "modifier_cd")) %>%
+    dplyr::distinct() %>%
+    dplyr::filter(!is.na(concept_cd)) %>%
+    dplyr::mutate(concept_cd = stringr::str_c("CIM:", concept_cd),
+           provider_id = stringr::str_c("STRUCT:", provider_id),
+           modifier_cd = stringr::str_c("CIM:", modifier_cd),
+           instance_num = 1) %>%
+    dplyr::mutate(patient_ide = ifelse(patient_ide %>% as.numeric > 2^32,
+                                patient_ide %>% stringr::str_sub(2),
+                                patient_ide)) %>%
+    add_observations(project)
+}
+
+import_actes <- function(actes, project)
+{
+  # Observations : Actes
+  actes %>%
+    stats::setNames(c("patient_ide", "encounter_ide", "provider_id", "concept_cd", "start_date")) %>%
+    dplyr::distinct() %>%
+    dplyr::filter(!is.na(concept_cd)) %>%
+    dplyr::mutate(concept_cd = stringr::str_c("CCAM:", concept_cd),
+           provider_id = stringr::str_c("STRUCT:", provider_id),
+           modifier_cd = "@",
+           instance_num = 1) %>%
+    dplyr::mutate(patient_ide = ifelse(patient_ide %>% as.numeric > 2^32,
+                                patient_ide %>% stringr::str_sub(2),
+                                patient_ide)) %>%
+    add_observations(project)
 }
+