Removed specific code

R/fresh_install.R

@@ -40,343 +40,22 @@ fresh_install <- function(admin, pass, domain_id, domain_name)
   # Prepare to clone i2b2demodata
   service("pg", "restart")
 
-  add_project("CHRU", "CHRU - Tous services")
+  add_project("main", "Main Project")
 
-  add_user_roles("i2b2", "demouser", "maxx", "CHRU", c("MANAGER", "USER", "DATA_PROT"))
+  add_user_roles("i2b2", "demouser", "admin", "main", c("MANAGER", "USER", "DATA_PROT"))
 
   # Clean old users
   delete_users(c("i2b2","demo"))
 
   # Add ontologies
-  add_ont("Diagnostics", "CIM")
-  add_ont("Actes", "CCAM")
-  add_ont("Patients", "PAT")
-  add_ont("Hospitalisations", "HOS")
-  add_ont("Services", "STRUCT")
-  add_ont("Biologies", "BIO")
+  # add_ont("Name", "Scheme")
 
   # Populate the ontologies
-  populate_ont(readr::read_csv("..inst/cim.ont"), readr::read_csv("..inst/cim.modi"), "CIM")
-  populate_ont(readr::read_csv("../inst/ccam.ont"), modi = NULL, "CCAM")
-  populate_ont(readr::read_csv("../inst/patients.ont"), modi = NULL, "PAT", include_code = F)
-  populate_ont(readr::read_csv("../inst/hospit.ont"), modi = NULL, "HOS", include_code = F)
-  populate_ont(readr::read_csv("../inst/struct.ont"), modi = NULL, "STRUCT", def_facttablecolumn = "provider_id", def_tablename = "provider_dimension", def_columnname = "provider_path")
-  populate_ont(readr::read_csv("../inst/bio.ont"), modi = NULL, "BIO", include_code = F)
+  # populate_ont(readr::read_csv(".ont"), readr::read_csv(".modi"), "Scheme")
 
   # Populate the concept/provider tables needed
-  add_ontologies("CHRU")
+  # populate_concept(readr::read_csv(".ont", readr::read_csv(".modi", "Scheme", "main")))
 
   # Restart wildfly
   service("jboss", "restart")
 }
-
-accounts_obgyn <- function()
-{
-  "CHRU" -> main
-  620 -> top_project
-  seq(6040, 6100, 10) -> projects
-
-  "maxx" -> admin
-
-  "obgyn" -> top_user
-  "Gynécologie-Obstétrique" -> top_name
-
-  c("amp", "cancero", "ortho", "ante", "endoc", "post", "nn") -> users
-  c("AMP Clinique", "Gynécologie et Cancérologie", "Orthogénie", "Anténatal", "Endocrinologie Maternité", "Post-natal", "Nouveaux-nés") -> names
-
-  "med_amp" -> bottom_user
-  "Médecin AMP" -> bottom_name
-
-## Admin
-# MANAGER on main
-  admin %>%
-    purrr::map(~add_user_roles("i2b2", "demouser", .x, main,  c("MANAGER", "USER", "DATA_PROT")))
-
-# MANAGER on top_project
-  admin %>%
-    purrr::map(~add_user_roles("i2b2", "demouser", .x, top_project, c("MANAGER", "USER", "DATA_PROT")))
-
-# MANAGER on projects
-  admin %>%
-    purrr::map2(projects, ~add_user_roles("i2b2", "demouser", .x, .y, c("MANAGER", "USER", "DATA_PROT")))
-
-
-## Top user
-# Add top user
-  top_user %>%
-    purrr::map2(top_name, ~add_user("i2b2", "demouser", .x, .y, "", .x))
-
-# DATA_AGG on main
-  top_user %>%
-    purrr::map(~add_user_roles("i2b2", "demouser", .x, main, c("USER", "DATA_AGG")))
-
-# MANAGER on top_project
-  top_user %>%
-    purrr::map(~add_user_roles("i2b2", "demouser", .x, top_project, c("MANAGER", "USER", "DATA_PROT")))
-
-# MANAGER on projects
-  top_user %>%
-    purrr::map2(projects, ~add_user_roles("i2b2", "demouser", .x, .y, c("MANAGER", "USER", "DATA_PROT")))
-
-
-## Users
-# Add users
-  users %>%
-  purrr::map2(names, ~add_user("i2b2", "demouser", .x, .y, "", .x))
-
-# DATA_OBFSC on main
-  users %>%
-    purrr::map(~add_user_roles("i2b2", "demouser", .x, main, c("USER", "DATA_OBFSC")))
-
-# DATA_AGG on top_project
-  users %>%
-    purrr::map(~add_user_roles("i2b2", "demouser", .x, top_project, c("USER", "DATA_AGG")))
-
-# MANAGER on projects
-  users %>%
-    purrr::map2(projects, ~add_user_roles("i2b2", "demouser", .x, .y, c("MANAGER", "USER", "DATA_PROT")))
-
-
-## Bottom users
-# Add user
-  bottom_user %>%
-    purrr::map2(bottom_name, ~add_user("i2b2", "demouser", .x, .y, "", .x))
-
-# DATA_OBFSC on main
-  bottom_user %>%
-    purrr::map(~add_user_roles("i2b2", "demouser", .x, main, c("USER", "DATA_OBFSC")))
-
-# DATA_OBFSC on top_project
-  bottom_user %>%
-    purrr::map(~add_user_roles("i2b2", "demouser", .x, top_project, c("USER", "DATA_OBFSC")))
-
-# DATA_AGG on project
-  bottom_user %>%
-    purrr::map2("amp", ~add_user_roles("i2b2", "demouser", .x, .y, c("USER", "DATA_AGG")))
-}
-
-#pop_project(620, seq(6040, 6100, 10), "/manip/pims16.csv", "/manip/diags16.csv", "/manip/actes16.csv", "/manip/mensurations16.csv", "/manip/bios16.csv")
-#pop_project(620, seq(6040, 6100, 10), "/manip/pims17.csv", "/manip/diags17.csv", "/manip/actes17.csv", "/manip/mensurations17.csv", "/manip/bios17.csv")
-
-pop_projects <- function(top_project, projects, patients_file, diagnostics_file, actes_file, mensurations_file, bios_file)
-{
-  c(top_project, projects) %>%
-    purrr::map(add_ontologies)
-
-  read_patients(patients_file) %>%
-    dplyr::filter(project %in% projects) ->
-  patients
-
-  patients %>%
-    import_patients_visits(top_project)
-
-  read_diagnostics(diagnostics_file) %>%
-    dplyr::semi_join(patients, by = c("patient_ide", "encounter_ide")) %>%
-    import_diagnostics(top_project)
-
-  read_actes(actes_file) %>%
-    dplyr::semi_join(patients, by = c("patient_ide", "encounter_ide")) %>%
-  import_actes(top_project)
-
-  read_mensurations(mensurations_file) %>%
-    dplyr::semi_join(patients, by = c("patient_ide", "encounter_ide")) %>%
-  import_mensurations(patients, top_project)
-
-  read_bios(bios_file, n_max = 5e6) %>%
-    dplyr::semi_join(patients, by = c("patient_ide", "encounter_ide")) %>%
-  import_bios(patients, top_project)
-
-  read_bios(bios_file, skip = 5e6) %>%
-    dplyr::semi_join(patients, by = c("patient_ide", "encounter_ide")) %>%
-  import_bios(patients, top_project)
-
-  projects %>%
-    purrr::map(function(x)
-        {
-          read_patients(patients_file) %>%
-            dplyr::filter(project == x) ->
-              patients
-
-            patients %>%
-              import_patients_visits(x)
-
-            read_diagnostics(diagnostics_file) %>%
-              dplyr::semi_join(patients, by = c("patient_ide", "encounter_ide")) %>%
-              import_diagnostics(x)
-
-            read_actes(actes_file) %>%
-              dplyr::semi_join(patients, by = c("patient_ide", "encounter_ide")) %>%
-              import_actes(x)
-
-            read_mensurations(mensurations_file) %>%
-              dplyr::semi_join(patients, by = c("patient_ide", "encounter_ide")) %>%
-              import_mensurations(patients, x)
-
-            read_bios(bios_file, n_max = 5e6) %>%
-              dplyr::semi_join(patients, by = c("patient_ide", "encounter_ide")) %>%
-              import_bios(patients, x)
-
-            read_bios(bios_file, skip = 5e6) %>%
-              dplyr::semi_join(patients, by = c("patient_ide", "encounter_ide")) %>%
-              import_bios(patients, x)
-        })
-}
-
-#pop_chru("CHRU", "/manip/pims16.csv", "/manip/diags16.csv", "/manip/actes16.csv", "/manip/mensurations16.csv", "/manip/bios16.csv")
-#pop_chru("CHRU", "/manip/pims17.csv", "/manip/diags17.csv", "/manip/actes17.csv", "/manip/mensurations17.csv", "/manip/bios17.csv")
-
-pop_main <- function(main, patients_file, diagnostics_file, actes_file, mensurations_file, bios_file)
-{
-  read_patients(patients_file) -> patients
-
-  patients %>%
-  import_patients_visits(main)
-
-  read_diagnostics(diagnostics_file) %>%
-  add_observations(main)
-
-  read_actes(actes_file) %>%
-  add_observations(main)
-
-  read_mensurations(mensurations_file) %>%
-  import_mensurations(patients, main)
-
-  read_bios(bios_file, n_max = 5e6) %>%
-  import_bios(patients, main)
-
-  read_bios(bios_file, skip = 5e6) %>%
-  import_bios(patients, main)
-}
-
-read_patients <- function(file)
-{
-  readr::read_csv(file, col_types = readr::cols(.default = readr::col_character())) %>%
-    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(patient_ide   = sanitize_patient(patient_ide),
-                  encounter_ide = sanitize_encounter(encounter_ide, start_date),
-                  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"),
-                  sex_cd        = ifelse(sex_cd == "1", "M", "F"),
-                  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"),
-                  rum_start     = rum_start  %>% as.Date(format = "%Y/%m/%d %H:%M:%S"),
-                  rum_end       = rum_end    %>% as.Date(format = "%Y/%m/%d %H:%M:%S"),
-                  provider_id   = stringr::str_c("STRUCT:", provider_id))
-}
-
-read_diagnostics <- function(file)
-{
-  readr::read_csv(file, col_types = readr::cols(.default = readr::col_character())) %>%
-    stats::setNames(c("patient_ide",
-                      "encounter_ide",
-                      "enc_start_date",
-                      "start_date",
-                      "end_date",
-                      "provider_id",
-                      "concept_cd",
-                      "modifier_cd")) %>%
-    dplyr::mutate(encounter_ide = sanitize_encounter(encounter_ide, enc_start_date),
-                  patient_ide   = sanitize_patient(patient_ide),
-                  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"),
-                  provider_id   = stringr::str_c("STRUCT:", provider_id),
-                  concept_cd    = stringr::str_c("CIM:", concept_cd),
-                  modifier_cd   = stringr::str_c("CIM:", modifier_cd)) %>%
-    dplyr::select(-enc_start_date)
-}
-
-read_actes <- function(file)
-{
-  readr::read_csv(file, col_types = readr::cols(.default = readr::col_character())) %>%
-    stats::setNames(c("patient_ide",
-                      "encounter_ide",
-                      "enc_start_date",
-                      "provider_id",
-                      "concept_cd",
-                      "start_date")) %>%
-  dplyr::mutate(encounter_ide = sanitize_encounter(encounter_ide, enc_start_date),
-                patient_ide   = sanitize_patient(patient_ide),
-                provider_id   = stringr::str_c("STRUCT:", provider_id),
-                concept_cd    = stringr::str_c("CCAM:", concept_cd),
-                modifier_cd   = "@",
-                start_date    = start_date %>% as.Date(format = "%Y/%m/%d %H:%M:%S")) %>%
-  dplyr::select(-enc_start_date)
-}
-
-read_mensurations <- function(file)
-{
-  readr::read_csv(file, col_types = readr::cols(.default = readr::col_character())) %>%
-    stats::setNames(c("patient_ide",
-                      "encounter_ide",
-                      "enc_start_date",
-                      "poids",
-                      "taille",
-                      "IMC")) %>%
-    dplyr::mutate(patient_ide = sanitize_patient(patient_ide),
-                  encounter_ide = sanitize_encounter(encounter_ide, enc_start_date)) %>%
-    dplyr::select(-enc_start_date) %>%
-    tidyr::gather(concept_cd, nval_num, poids, taille, IMC) %>%
-    dplyr::filter(!is.na(nval_num)) %>%
-    dplyr::mutate(concept_cd  = stringr::str_c("HOS:", concept_cd),
-                  modifier_cd = "@",
-                  valtype_cd  = "N",
-                  tval_char   = "E",
-                  nval_num    = nval_num %>% stringr::str_replace(",", "."))
-}
-
-read_bios <- function(file, ...)
-{
-  readr::read_csv("../inst/bio.map") -> mapping
-
-  readr::read_csv(file, col_types = readr::cols(.default = readr::col_character()), ...) %>%
-    stats::setNames(c("patient_ide",
-                      "encounter_ide",
-                      "enc_start_date",
-                      "start_date",
-                      "concept_cd",
-                      "nval_num")) %>%
-    dplyr::left_join(mapping, by = c("concept_cd" = "from")) %>%
-    dplyr::mutate(encounter_ide = sanitize_encounter(encounter_ide, enc_start_date),
-                  patient_ide   = sanitize_patient(patient_ide),
-                  start_date    = start_date %>% as.Date(format = "%Y/%m/%d %H:%M:%S"),
-                  modifier_cd   = "@",
-                  concept_cd    = ifelse(!is.na(to), to, concept_cd),
-                  concept_cd    = stringr::str_c("BIO:", concept_cd)) %>%
-    dplyr::select(-to, -enc_start_date)
-}
-
-sanitize_encounter <- function(encounter_ide, start_date)
-{
-  start_date <- start_date %>% as.Date(format = "%Y/%m/%d %H:%M:%S")
-
-  ifelse(encounter_ide %>% stringr::str_detect("\\."),
-         stringr::str_c(encounter_ide, lubridate::day(start_date) %>% stringr::str_pad(2, "left", "0")),
-         encounter_ide)
-}
-
-sanitize_patient <- function(patient_ide)
-{
-  ifelse(patient_ide %>% as.numeric > 2^32,
-         patient_ide %>% stringr::str_sub(2),
-         patient_ide)
-}
-
-add_ontologies <- function(project)
-{
-  populate_concept(readr::read_csv("../inst/cim.ont")     , readr::read_csv("../inst/cim.modi"), "CIM" , project)
-  populate_concept(readr::read_csv("../inst/ccam.ont")    , modi = NULL                        , "CCAM", project)
-  populate_concept(readr::read_csv("../inst/bio.ont")     , modi = NULL                        , "BIO" , project)
-  populate_provider(readr::read_csv("../inst/struct.ont") , "STRUCT"                           , project)
-  populate_concept(readr::read_csv("../inst/hospit.ont")  , modi = NULL                        , "HOS" , project)
-  populate_concept(readr::read_csv("../inst/patients.ont"), modi = NULL                        , "PAT" , project)
-}