Safely insert complete data for many hospitals from the same year into the database.

This functions wraps the function qb_extract_one_clinic into a broader structure to ensure that possible errors are captured and logged and that all specified XML-files are processed.

qb_extract_many_clinics(
  conn = NULL,
  xml_file_names = NULL,
  xml_schema_path = NULL,
  global_hospital_id = NULL,
  years_lookuptable = c(`1` = 2015, `2` = 2016, `3` = 2017, `4` = 2018, `5` = 2019),
  db_name = "gbadata",
  logging = FALSE,
  log_dir = "logs"
)

Arguments

conn	A RMariaDB-connection object (based on the DBI-package) to the database where the GBA data is stored.
xml_file_names	A character vector containing the paths to the XML-files containing the detailed report (not the ones named "bund" or "Land"!).
xml_schema_path	Here, the path to the XML schema file for the year in question is needed which is used at the beginning of the parsing attempt to automatically check the integrity of the XML-file against the schema. The schema files are available from the GBA.
global_hospital_id	A data frame that was manually constructed, which comprises a list of all hospitals with all available reports starting from 2015 to 2019. Each entry gives the XML-filename, an ID that identifies the hospital in each year, an ID that is the same over all years, the IK number, the location number, the year, the name of the hospital, the original name in the XML-file, the state where the hospital is located, latitude and longitude.
years_lookuptable	A named vector comprising the years from 2015 to 2019: Default is c("1" = 2015, "2" = 2016, "3" = 2017, "4" = 2018, "5" = 2019).
db_name	The name of the database as a single string value. This is used to confirm that one is connected to the desired database. Defaults to "gbadata".
logging	A boolean value indicating if the results / errors of the data ingestion should be written to a log-file. Defaults to FALSE.
log_dir	A string specifying the directory where a log file should be placed. Defaults to "logs".

Value

As this is a wrapper function which uses qb_extract_one_clinic together with safely to produce a list with a result (the string returned by qb_extract_one_clinic) or an error-message, which is then used in a map-function, the result is a nested list with as many entries as XML-file names are provided as input.

Examples

if (FALSE) {

con <- dbConnect(RMariaDB::MariaDB(),
                 host     = "localhost",
                 port     = 3306,
                 username = keyring::key_list("mysql-localhost")[1,2],
                 password = keyring::key_get("mysql-localhost", "dataadmin"),
                 dbname   = "gbadata")

GlobalHospitalID <- readxl::read_excel("./00-data/GlobalHospitalID.xlsx",
                                       col_types = c(rep("text", times = 9),
                                       "numeric",
                                       "numeric"))
GlobalHospitalID <- GlobalHospitalID %>%
     mutate(idHospitalDataYear = case_when(
            year == "2015" ~ 1L,
            year == "2016" ~ 2L,
            year == "2017" ~ 3L,
            year == "2018" ~ 4L,
            year == "2019" ~ 5L
            ))

reports_detailed <- list.files("../2019_v2/Berichte-Teile-A-B-C/",
                               pattern = "-xml\\.xml$", full.names = TRUE)
XML_Schema_path <-
    "L:/19_GBA-QB/Servicedateien_2019/2020-10-07_Anlage-5_XML_Schema-BJ-2019.xsd"


results_2019 <- qb_extract_many_clinics(con,
                                        xml_file_names = reports_detailed,
                                        xml_schema_path = XML_Schema_path,
                                        global_hospital_id = GlobalHospitalID)

}