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R2b2/R/fresh_install.R

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  1. #' Make a fresh install from the base VM

  2. #'

  3. #' Make a fresh install from the base VM

  4. #'

  5. #' Set the permissions,

  6. #' create the admin account for the system, database, and i2b2

  7. #' Set the domain and project

  8. #' Delete the default users

  9. #' Clear the metadata database, and the *_dimension tables in demodata

  10. #'

  11. #' @param admin The admin account for the PostgreSQL database

  12. #' @param pass the password for the admin account

  13. #' @param domain_id The desired domain_id

  14. #' @param domain_name The desired domain_name

  15. #' @export

  16. fresh_install <- function(admin, pass, domain_id, domain_name)

  17. {

  18.   # System

  19.   set_permissions()

  20. 

  21.   create_admin(admin, pass)

  22. 

  23.   # Clear the default install

  24.   clear_webclient()

  25. 

  26.   clear_default_workdata()

  27. 

  28.   clear_default_metadata()

  29. 

  30.   clear_default_imdata()

  31. 

  32.   clear_default_demodata()

  33. 

  34.   # Set the new domain

  35.   set_domain(domain_id, domain_name)

  36. 

  37.   # Add new admin

  38.   add_users("i2b2", "demouser", data.frame(id = admin, password = pass, name = admin, email = "", role = "ADMIN", project = "@"))

  39. 

  40.   # Prepare to clone i2b2demodata

  41.   service("pg", "restart")

  42. 

  43.   add_project("CHRU", "CHRU - Tous services")

  44. 

  45.   add_user_roles("i2b2", "demouser", "maxx", "CHRU", c("MANAGER", "USER", "DATA_PROT"))

  46. 

  47.   # Clean old users

  48.   delete_users(c("i2b2","demo"))

  49. 

  50.   # Add ontologies

  51.   add_ont("Diagnostics", "CIM")

  52.   add_ont("Actes", "CCAM")

  53.   add_ont("Patients", "PAT")

  54.   add_ont("Hospitalisations", "HOS")

  55.   add_ont("Services", "STRUCT")

  56.   add_ont("Biologies", "BIO")

  57. 

  58.   # Populate the ontologies

  59.   populate_ont(readr::read_csv("..inst/cim.ont"), readr::read_csv("..inst/cim.modi"), "CIM")

  60.   populate_ont(readr::read_csv("../inst/ccam.ont"), modi = NULL, "CCAM")

  61.   populate_ont(readr::read_csv("../inst/patients.ont"), modi = NULL, "PAT", include_code = F)

  62.   populate_ont(readr::read_csv("../inst/hospit.ont"), modi = NULL, "HOS", include_code = F)

  63.   populate_ont(readr::read_csv("../inst/struct.ont"), modi = NULL, "STRUCT")

  64.   populate_ont(readr::read_csv("../inst/bio.ont"), modi = NULL, "BIO", include_code = F)

  65. 

  66.   # Populate the concept/provider tables needed

  67.   add_ontologies("CHRU")

  68. 

  69.   # Restart wildfly

  70.   service("jboss", "restart")

  71. }

  72. 

  73. accounts_obgyn <- function()

  74. {

  75.   add_user("i2b2", "demouser", "obgyn", "Gynécologie-Obstétrique", "", "obgyn")

  76.   add_user("i2b2", "demouser", "amp", "AMP Clinique", "", "amp")

  77.   add_user("i2b2", "demouser", "cancero", "Gynécologie et Cancérologie", "", "cancero")

  78.   add_user("i2b2", "demouser", "ortho", "Orthogénie", "", "ortho")

  79.   add_user("i2b2", "demouser", "ante", "Anténatal", "", "ante")

  80.   add_user("i2b2", "demouser", "endoc", "Endocrinologie Maternité", "", "endoc")

  81.   add_user("i2b2", "demouser", "post", "Post-natal", "", "post")

  82.   add_user("i2b2", "demouser", "nn", "Nouveaux-nés", "", "nn")

  83. 

  84.   add_user("i2b2", "demouser", "med_amp", "Médecin AMP", "", "med_amp")

  85. 

  86.   add_user_roles("i2b2", "demouser", "maxx", "620", c("MANAGER", "USER", "DATA_PROT"))

  87.   add_user_roles("i2b2", "demouser", "maxx", "6040", c("MANAGER", "USER", "DATA_PROT"))

  88.   add_user_roles("i2b2", "demouser", "maxx", "6050", c("MANAGER", "USER", "DATA_PROT"))

  89.   add_user_roles("i2b2", "demouser", "maxx", "6060", c("MANAGER", "USER", "DATA_PROT"))

  90.   add_user_roles("i2b2", "demouser", "maxx", "6070", c("MANAGER", "USER", "DATA_PROT"))

  91.   add_user_roles("i2b2", "demouser", "maxx", "6080", c("MANAGER", "USER", "DATA_PROT"))

  92.   add_user_roles("i2b2", "demouser", "maxx", "6090", c("MANAGER", "USER", "DATA_PROT"))

  93.   add_user_roles("i2b2", "demouser", "maxx", "6100", c("MANAGER", "USER", "DATA_PROT"))

  94. 

  95.   add_user_roles("i2b2", "demouser", "obgyn", "CHRU", c("USER", "DATA_AGG"))

  96.   add_user_roles("i2b2", "demouser", "obgyn", "620", c("MANAGER", "USER", "DATA_PROT"))

  97.   add_user_roles("i2b2", "demouser", "obgyn", "6040", c("MANAGER", "USER", "DATA_PROT"))

  98.   add_user_roles("i2b2", "demouser", "obgyn", "6050", c("MANAGER", "USER", "DATA_PROT"))

  99.   add_user_roles("i2b2", "demouser", "obgyn", "6060", c("MANAGER", "USER", "DATA_PROT"))

  100.   add_user_roles("i2b2", "demouser", "obgyn", "6070", c("MANAGER", "USER", "DATA_PROT"))

  101.   add_user_roles("i2b2", "demouser", "obgyn", "6080", c("MANAGER", "USER", "DATA_PROT"))

  102.   add_user_roles("i2b2", "demouser", "obgyn", "6090", c("MANAGER", "USER", "DATA_PROT"))

  103.   add_user_roles("i2b2", "demouser", "obgyn", "6100", c("MANAGER", "USER", "DATA_PROT"))

  104. 

  105.   add_user_roles("i2b2", "demouser", "amp", "CHRU", c("USER", "DATA_OBFSC"))

  106.   add_user_roles("i2b2", "demouser", "amp", "620", c("USER", "DATA_AGG"))

  107.   add_user_roles("i2b2", "demouser", "amp", "6040", c("MANAGER", "USER", "DATA_PROT"))

  108. 

  109.   add_user_roles("i2b2", "demouser", "cancero", "CHRU", c("USER", "DATA_OBFSC"))

  110.   add_user_roles("i2b2", "demouser", "cancero", "620", c("USER", "DATA_AGG"))

  111.   add_user_roles("i2b2", "demouser", "cancero", "6050", c("MANAGER", "USER", "DATA_PROT"))

  112. 

  113.   add_user_roles("i2b2", "demouser", "ortho", "CHRU", c("USER", "DATA_OBFSC"))

  114.   add_user_roles("i2b2", "demouser", "ortho", "620", c("USER", "DATA_AGG"))

  115.   add_user_roles("i2b2", "demouser", "ortho", "6060", c("MANAGER", "USER", "DATA_PROT"))

  116. 

  117.   add_user_roles("i2b2", "demouser", "ante", "CHRU", c("USER", "DATA_OBFSC"))

  118.   add_user_roles("i2b2", "demouser", "ante", "620", c("USER", "DATA_AGG"))

  119.   add_user_roles("i2b2", "demouser", "ante", "6070", c("MANAGER", "USER", "DATA_PROT"))

  120. 

  121.   add_user_roles("i2b2", "demouser", "endoc", "CHRU", c("USER", "DATA_OBFSC"))

  122.   add_user_roles("i2b2", "demouser", "endoc", "620", c("USER", "DATA_AGG"))

  123.   add_user_roles("i2b2", "demouser", "endoc", "6080", c("MANAGER", "USER", "DATA_PROT"))

  124. 

  125.   add_user_roles("i2b2", "demouser", "post", "CHRU", c("USER", "DATA_OBFSC"))

  126.   add_user_roles("i2b2", "demouser", "post", "620", c("USER", "DATA_AGG"))

  127.   add_user_roles("i2b2", "demouser", "post", "6090", c("MANAGER", "USER", "DATA_PROT"))

  128. 

  129.   add_user_roles("i2b2", "demouser", "nn", "CHRU", c("USER", "DATA_OBFSC"))

  130.   add_user_roles("i2b2", "demouser", "nn", "620", c("USER", "DATA_AGG"))

  131.   add_user_roles("i2b2", "demouser", "nn", "6100", c("MANAGER", "USER", "DATA_PROT"))

  132. 

  133.   add_user_roles("i2b2", "demouser", "med_amp", "CHRU", c("USER", "DATA_OBFSC"))

  134.   add_user_roles("i2b2", "demouser", "med_amp", "620", c("USER", "DATA_OBFSC"))

  135.   add_user_roles("i2b2", "demouser", "med_amp", "6040", c("USER", "DATA_AGG"))

  136. }

  137. 

  138. pop_obgyn <- function()

  139. {

  140.   UM <- seq(6040, 6100, 10)

  141. 

  142.   c(UM, 620) %>%

  143.     purrr::map(add_ontologies)

  144. 

  145. # 2016

  146.   readr::read_csv("/manip/pims16.csv", col_types = readr::cols(.default = readr::col_character())) %>%

  147.     stats::setNames(c("patient_ide", "encounter_ide", "start_date", "end_date", "sex_cd", "birth_date", "death_date", "rum_start", "rum_end", "provider_id", "project")) %>%

  148.     dplyr::filter(project %in% UM) ->

  149.   patients

  150. 

  151.   patients %>%

  152.     import_patients_visits(620)

  153. 

  154.   readr::read_csv("/manip/diags16.csv", col_types = readr::cols(.default = readr::col_character())) %>%

  155.     stats::setNames(c("patient_ide", "encounter_ide", "start_date", "end_date", "provider_id", "concept_cd", "modifier_cd")) %>%

  156.     dplyr::semi_join(patients, by = c("patient_ide", "encounter_ide")) %>%

  157.     import_diagnostics(620)

  158. 

  159.   readr::read_csv("/manip/actes16.csv", col_types = readr::cols(.default = readr::col_character())) %>%

  160.     stats::setNames(c("patient_ide", "encounter_ide", "provider_id", "concept_cd", "start_date")) %>%

  161.     dplyr::semi_join(patients, by = c("patient_ide", "encounter_ide")) %>%

  162.   import_actes(620)

  163. 

  164.   readr::read_csv("/manip/mensurations16.csv", col_types = readr::cols(.default = readr::col_character())) %>%

  165.     stats::setNames(c("patient_ide", "encounter_ide", "poids", "taille", "IMC")) %>%

  166.     dplyr::semi_join(patients, by = c("patient_ide", "encounter_ide")) %>%

  167.   import_mensurations(patients, 620)

  168. 

  169.   readr::read_csv("/manip/bio16_1.csv", col_types = readr::cols(.default = readr::col_character())) %>%

  170.     stats::setNames(c("patient_ide", "encounter_ide", "start_date", "concept_cd", "nval_num")) %>%

  171.     dplyr::semi_join(patients, by = c("patient_ide", "encounter_ide")) %>%

  172.   import_bios(patients, 620)

  173. 

  174.   readr::read_csv("/manip/bio16_2.csv", col_types = readr::cols(.default = readr::col_character())) %>%

  175.     stats::setNames(c("patient_ide", "encounter_ide", "start_date", "concept_cd", "nval_num")) %>%

  176.     dplyr::semi_join(patients, by = c("patient_ide", "encounter_ide")) %>%

  177.   import_bios(patients, 620)

  178. 

  179. # 2017

  180.   readr::read_csv("/manip/pims17.csv", col_types = readr::cols(.default = readr::col_character())) %>%

  181.     stats::setNames(c("patient_ide", "encounter_ide", "start_date", "end_date", "sex_cd", "birth_date", "death_date", "rum_start", "rum_end", "provider_id", "project")) %>%

  182.     dplyr::filter(project %in% UM) ->

  183.   patients

  184. 

  185.   patients %>%

  186.     import_patients_visits(620)

  187. 

  188.   readr::read_csv("/manip/diags17.csv", col_types = readr::cols(.default = readr::col_character())) %>%

  189.     stats::setNames(c("patient_ide", "encounter_ide", "start_date", "end_date", "provider_id", "concept_cd", "modifier_cd")) %>%

  190.     dplyr::semi_join(patients, by = c("patient_ide", "encounter_ide")) %>%

  191.     import_diagnostics(620)

  192. 

  193.   readr::read_csv("/manip/actes17.csv", col_types = readr::cols(.default = readr::col_character())) %>%

  194.     stats::setNames(c("patient_ide", "encounter_ide", "provider_id", "concept_cd", "start_date")) %>%

  195.     dplyr::semi_join(patients, by = c("patient_ide", "encounter_ide")) %>%

  196.   import_actes(620)

  197. 

  198.   readr::read_csv("/manip/mensurations17.csv", col_types = readr::cols(.default = readr::col_character())) %>%

  199.     stats::setNames(c("patient_ide", "encounter_ide", "poids", "taille", "IMC")) %>%

  200.     dplyr::semi_join(patients, by = c("patient_ide", "encounter_ide")) %>%

  201.   import_mensurations(patients, 620)

  202. 

  203.   readr::read_csv("/manip/bios17.csv", col_types = readr::cols(.default = readr::col_character())) %>%

  204.     stats::setNames(c("patient_ide", "encounter_ide", "start_date", "concept_cd", "nval_num")) %>%

  205.     dplyr::semi_join(patients, by = c("patient_ide", "encounter_ide")) %>%

  206.   import_bios(patients, 620)

  207. 

  208.   UM %>%

  209.     purrr::map(function(x)

  210.         {

  211.           # 2016

  212.           readr::read_csv("/manip/pims16.csv", col_types = readr::cols(.default = readr::col_character())) %>%

  213.             stats::setNames(c("patient_ide", "encounter_ide", "start_date", "end_date", "sex_cd", "birth_date", "death_date", "rum_start", "rum_end", "provider_id", "project")) %>%

  214.             dplyr::filter(project == x) ->

  215.               patients

  216. 

  217.             patients %>%

  218.               import_patients_visits(x)

  219. 

  220.             readr::read_csv("/manip/diags16.csv", col_types = readr::cols(.default = readr::col_character())) %>%

  221.               stats::setNames(c("patient_ide", "encounter_ide", "start_date", "end_date", "provider_id", "concept_cd", "modifier_cd")) %>%

  222.               dplyr::semi_join(patients, by = c("patient_ide", "encounter_ide")) %>%

  223.               import_diagnostics(x)

  224. 

  225.             readr::read_csv("/manip/actes16.csv", col_types = readr::cols(.default = readr::col_character())) %>%

  226.               stats::setNames(c("patient_ide", "encounter_ide", "provider_id", "concept_cd", "start_date")) %>%

  227.               dplyr::semi_join(patients, by = c("patient_ide", "encounter_ide")) %>%

  228.               import_actes(x)

  229. 

  230.             readr::read_csv("/manip/mensurations16.csv", col_types = readr::cols(.default = readr::col_character())) %>%

  231.               stats::setNames(c("patient_ide", "encounter_ide", "poids", "taille", "IMC")) %>%

  232.               dplyr::semi_join(patients, by = c("patient_ide", "encounter_ide")) %>%

  233.               import_mensurations(patients, x)

  234. 

  235.             readr::read_csv("/manip/bio16_1.csv", col_types = readr::cols(.default = readr::col_character())) %>%

  236.               stats::setNames(c("patient_ide", "encounter_ide", "start_date", "concept_cd", "nval_num")) %>%

  237.               dplyr::semi_join(patients, by = c("patient_ide", "encounter_ide")) %>%

  238.               import_bios(patients, x)

  239. 

  240.             readr::read_csv("/manip/bio16_2.csv", col_types = readr::cols(.default = readr::col_character())) %>%

  241.               stats::setNames(c("patient_ide", "encounter_ide", "start_date", "concept_cd", "nval_num")) %>%

  242.               dplyr::semi_join(patients, by = c("patient_ide", "encounter_ide")) %>%

  243.               import_bios(patients, x)

  244. 

  245.             # 2017

  246.             readr::read_csv("/manip/pims17.csv", col_types = readr::cols(.default = readr::col_character())) %>%

  247.               stats::setNames(c("patient_ide", "encounter_ide", "start_date", "end_date", "sex_cd", "birth_date", "death_date", "rum_start", "rum_end", "provider_id", "project")) %>%

  248.               dplyr::filter(project == x) ->

  249.                 patients

  250. 

  251.               patients %>%

  252.                 import_patients_visits(x)

  253. 

  254.               readr::read_csv("/manip/diags17.csv", col_types = readr::cols(.default = readr::col_character())) %>%

  255.                 stats::setNames(c("patient_ide", "encounter_ide", "start_date", "end_date", "provider_id", "concept_cd", "modifier_cd")) %>%

  256.                 dplyr::semi_join(patients, by = c("patient_ide", "encounter_ide")) %>%

  257.                 import_diagnostics(x)

  258. 

  259.               readr::read_csv("/manip/actes17.csv", col_types = readr::cols(.default = readr::col_character())) %>%

  260.                 stats::setNames(c("patient_ide", "encounter_ide", "provider_id", "concept_cd", "start_date")) %>%

  261.                 dplyr::semi_join(patients, by = c("patient_ide", "encounter_ide")) %>%

  262.                 import_actes(x)

  263. 

  264.               readr::read_csv("/manip/mensurations17.csv", col_types = readr::cols(.default = readr::col_character())) %>%

  265.                 stats::setNames(c("patient_ide", "encounter_ide", "poids", "taille", "IMC")) %>%

  266.                 dplyr::semi_join(patients, by = c("patient_ide", "encounter_ide")) %>%

  267.                 import_mensurations(patients, x)

  268. 

  269.               readr::read_csv("/manip/bios17.csv", col_types = readr::cols(.default = readr::col_character())) %>%

  270.                 stats::setNames(c("patient_ide", "encounter_ide", "start_date", "concept_cd", "nval_num")) %>%

  271.                 dplyr::semi_join(patients, by = c("patient_ide", "encounter_ide")) %>%

  272.                 import_bios(patients, x)

  273. 

  274.         })

  275. }

  276. 

  277. pop_chru <- function()

  278. {

  279.   # 2016

  280.   read_patients("/manip/pims16.csv") -> patients

  281. 

  282.   patients %>%

  283.   import_patients_visits("CHRU")

  284. 

  285.   read_diagnostics("/manip/diags16.csv") %>%

  286.   add_observations("CHRU")

  287. 

  288.   read_actes("/manip/actes16.csv") %>%

  289.   add_observations("CHRU")

  290. 

  291.   read_mensurations("/manip/mensurations16.csv") %>%

  292.   import_mensurations(patients, "CHRU")

  293. 

  294.   read_bios("/manip/bio16_1.csv") %>%

  295.   import_bios(patients, "CHRU")

  296. 

  297.   read_bios("/manip/bio16_2.csv") %>%

  298.   import_bios(patients, "CHRU")

  299. 

  300. # 2017

  301.   read_patients("/manip/pims16.csv") -> patients

  302. 

  303.   patients %>%

  304.   import_patients_visits("CHRU")

  305. 

  306.   read_diagnostics("/manip/diags17.csv") %>%

  307.   add_observations("CHRU")

  308. 

  309.   read_actes("/manip/actes17.csv") %>%

  310.   add_observations("CHRU")

  311. 

  312.   read_mensurations("/manip/mensurations17.csv") %>%

  313.   import_mensurations(patients, "CHRU")

  314. 

  315.   read_bios("/manip/bios17.csv") %>%

  316.   import_bios(patients, "CHRU")

  317. }

  318. 

  319. read_patients <- function(file)

  320. {

  321.   readr::read_csv(file, col_types = readr::cols(.default = readr::col_character())) %>%

  322.     stats::setNames(c("patient_ide",

  323.                       "encounter_ide",

  324.                       "start_date",

  325.                       "end_date",

  326.                       "sex_cd",

  327.                       "birth_date",

  328.                       "death_date",

  329.                       "rum_start",

  330.                       "rum_end",

  331.                       "provider_id",

  332.                       "project")) %>%

  333.     dplyr::mutate(patient_ide   = sanitize_encounter(patient_ide),

  334.                   encounter_ide = sanitize_encounter(encounter_ide, start_date),

  335.                   start_date    = start_date %>% as.Date(format = "%Y/%m/%d %H:%M:%S"),

  336.                   end_date      = end_date   %>% as.Date(format = "%Y/%m/%d %H:%M:%S"),

  337.                   sex_cd        = ifelse(sex_cd == "1", "M", "F"),

  338.                   birth_date    = birth_date %>% as.Date(format = "%Y/%m/%d %H:%M:%S"),

  339.                   death_date    = death_date %>% as.Date(format = "%Y/%m/%d %H:%M:%S"),

  340.                   rum_start     = rum_start  %>% as.Date(format = "%Y/%m/%d %H:%M:%S"),

  341.                   rum_end       = rum_end    %>% as.Date(format = "%Y/%m/%d %H:%M:%S"),

  342.                   provider_id   = stringr::str_c("STRUCT:", provider_id))

  343. }

  344. 

  345. read_diagnostics <- function(file)

  346. {

  347.   readr::read_csv(file, col_types = readr::cols(.default = readr::col_character())) %>%

  348.     stats::setNames(c("patient_ide",

  349.                       "encounter_ide",

  350.                       "enc_start_date",

  351.                       "start_date",

  352.                       "end_date",

  353.                       "provider_id",

  354.                       "concept_cd",

  355.                       "modifier_cd")) %>%

  356.     dplyr::mutate(encounter_ide = sanitize_encounter(encounter_ide, enc_start_date),

  357.                   patient_ide   = sanitize_patient(patient_ide),

  358.                   start_date    = start_date %>% as.Date(format = "%Y/%m/%d %H:%M:%S"),

  359.                   end_date      = end_date   %>% as.Date(format = "%Y/%m/%d %H:%M:%S"),

  360.                   provider_id   = stringr::str_c("STRUCT:", provider_id),

  361.                   concept_cd    = stringr::str_c("CIM:", concept_cd),

  362.                   modifier_cd   = stringr::str_c("CIM:", modifier_cd)) %>%

  363.     dplyr::select(-enc_start_date)

  364. }

  365. 

  366. read_actes <- function(file)

  367. {

  368.   readr::read_csv(file, col_types = readr::cols(.default = readr::col_character())) %>%

  369.     stats::setNames(c("patient_ide",

  370.                       "encounter_ide",

  371.                       "enc_start_date",

  372.                       "provider_id",

  373.                       "concept_cd",

  374.                       "start_date")) %>%

  375.   dplyr::mutate(encounter_ide = sanitize_encounter(encounter_ide, enc_start_date),

  376.                 patient_ide   = sanitize_patient(patient_ide),

  377.                 provider_id   = stringr::str_c("STRUCT:", provider_id),

  378.                 concept_cd    = stringr::str_c("CCAM:", concept_cd),

  379.                 start_date    = start_date %>% as.Date(format = "%Y/%m/%d %H:%M:%S")) %>%

  380.   dplyr::select(-enc_start_date)

  381. }

  382. 

  383. read_mensurations <- function(file)

  384. {

  385.   readr::read_csv(file, col_types = readr::cols(.default = readr::col_character())) %>%

  386.     stats::setNames(c("patient_ide",

  387.                       "encounter_ide",

  388.                       "enc_start_date",

  389.                       "poids",

  390.                       "taille",

  391.                       "IMC")) %>%

  392.     dplyr::mutate(patient_ide = sanitize_patient(patient_ide),

  393.                   encounter_ide = sanitize_encounter(encounter_ide, enc_start_date)) %>%

  394.     dplyr::select(-enc_start_date) %>%

  395.     tidyr::gather(concept_cd, nval_num, poids, taille, IMC) %>%

  396.     dplyr::filter(!is.na(nval_num)) %>%

  397.     dplyr::mutate(concept_cd = stringr::str_c("HOS:", concept_cd),

  398.                   modifier_cd = "@",

  399.                   valtype_cd = "N",

  400.                   tval_char = "E",

  401.                   nval_num = nval_num %>% stringr::str_replace(",", "."))

  402. }

  403. 

  404. read_bios <- function(file)

  405. {

  406.   readr::read_csv("../inst/bio.map") -> mapping

  407. 

  408.   bios %>%

  409.     stats::setNames(c("patient_ide",

  410.                       "encounter_ide",

  411.                       "enc_start_date",

  412.                       "start_date",

  413.                       "concept_cd",

  414.                       "nval_num")) %>%

  415.     dplyr::left_join(mapping, by = c("concept_cd" = "from")) %>%

  416.     dplyr::mutate(encounter_ide = sanitize_encounter(encounter_ide, enc_start_date),

  417.                   patient_ide   = sanitize_patient(patient_ide),

  418.                   start_date    = start_date %>% as.Date(format = "%Y/%m/%d %H:%M:%S"),

  419.                   concept_cd    = ifelse(!is.na(to), to, concept_cd),

  420.                   concept_cd    = stringr::str_c("BIO:", concept_cd)) %>%

  421.     dplyr::select(-to, -enc_start_date)

  422. }

  423. 

  424. sanitize_encounter <- function(encounter_ide, start_date)

  425. {

  426.   start_date <- start_date %>% as.Date(format = "%Y/%m/%d %H:%M:%S")

  427. 

  428.   if (encounter_ide %>% stringr::str_detect("\\."))

  429.     encounter_ide <- stringr::str_c(encounter_ide, lubridate::day(start_date) %>% stringr::str_pad(2, "left", "0"))

  430. 

  431.   encounter_ide

  432. }

  433. 

  434. sanitize_patient <- function(patient_ide)

  435. {

  436.   if (patient_ide %>% as.numeric > 2^32)

  437.     patient_ide <- patient_ide %>% stringr::str_sub(2)

  438. 

  439.   patient_ide

  440. }

  441. 

  442. add_ontologies <- function(project)

  443. {

  444.   populate_concept(readr::read_csv("../inst/cim.ont"), readr::read_csv("../inst/cim.modi"), "CIM", project)

  445.   populate_concept(readr::read_csv("../inst/ccam.ont"), modi = NULL, "CCAM", project)

  446.   populate_concept(readr::read_csv("../inst/bio.ont"), modi = NULL, "BIO", project)

  447.   populate_provider(readr::read_csv("../inst/struct.ont"), "STRUCT", project)

  448.   populate_concept(readr::read_csv("../inst/hospit.ont"), modi = NULL, "HOS", project)

  449.   populate_concept(readr::read_csv("../inst/patients.ont"), modi = NULL, "PAT", project)

  450. }