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Introduction to csdb

Richard Aubrey White

2025-07-18

library(data.table)library(magrittr)

Concept

dbconnection<- csdb::DBConnection_v9$new(driver =Sys.getenv("CS9_DBCONFIG_DRIVER"),server =Sys.getenv("CS9_DBCONFIG_SERVER"),port =as.integer(Sys.getenv("CS9_DBCONFIG_PORT")),db =Sys.getenv("CS9_DBCONFIG_DB_ANON"),user =Sys.getenv("CS9_DBCONFIG_USER"),password =Sys.getenv("CS9_DBCONFIG_PASSWORD"),sslmode =Sys.getenv("CS9_DBCONFIG_SSLMODE"))dbconnection#> (disconnected)#>#> Driver:              PostgreSQL Unicode#> Server:              db#> Port:                5432#> DB:                  postgres#> User:                yourusername#> Password:            *********************#> Trusted connection:  xdbconnection$connect()dbconnection$connection#> <OdbcConnection> yourusername@db#>   Database: postgres#>   PostgreSQL Version: 17.0.5dbconnection$autoconnection#> <OdbcConnection> yourusername@db#>   Database: postgres#>   PostgreSQL Version: 17.0.5dbconnection#> (connected)#>#> Driver:              PostgreSQL Unicode#> Server:              db#> Port:                5432#> DB:                  postgres#> User:                yourusername#> Password:            *********************#> Trusted connection:  xdbconnection$disconnect()dbconnection$connection#> Error: external pointer is not validclass(dbconnection$connection)#> [1] "PostgreSQL"#> attr(,"package")#> [1] "odbc"class(dbconnection$autoconnection)#> [1] "PostgreSQL"#> attr(,"package")#> [1] "odbc"dbtable<- csdb::DBTable_v9$new(dbconfig =list(driver =Sys.getenv("CS9_DBCONFIG_DRIVER"),server =Sys.getenv("CS9_DBCONFIG_SERVER"),port =as.integer(Sys.getenv("CS9_DBCONFIG_PORT")),db =Sys.getenv("CS9_DBCONFIG_DB_ANON"),schema =Sys.getenv("CS9_DBCONFIG_SCHEMA_ANON"),user =Sys.getenv("CS9_DBCONFIG_USER"),password =Sys.getenv("CS9_DBCONFIG_PASSWORD"),sslmode =Sys.getenv("CS9_DBCONFIG_SSLMODE")  ),table_name ="anon_test",field_types =c("granularity_time"="TEXT","granularity_geo"="TEXT","country_iso3"="TEXT","location_code"="TEXT","border"="INTEGER","age"="TEXT","sex"="TEXT","isoyear"="INTEGER","isoweek"="INTEGER","isoyearweek"="TEXT","season"="TEXT","seasonweek"="DOUBLE","calyear"="INTEGER","calmonth"="INTEGER","calyearmonth"="TEXT","date"="DATE","covid19_cases_testdate_n"="INTEGER","covid19_cases_testdate_pr100000"="DOUBLE"    ),keys =c("granularity_time","location_code","date","age","sex"    ),indexes =list("ind1"=c("granularity_time","granularity_geo","country_iso3","location_code","border","age","sex","date","isoyear","isoweek","isoyearweek")    ),validator_field_types = csdb::validator_field_types_blank,validator_field_contents = csdb::validator_field_contents_blank)dbtable$drop_all_rows()dbtable$insert_data(csdb::nor_covid19_cases_by_time_location)dbtable$connect()dbtable$dbconnection$is_connected()#> [1] TRUEdbtable$tbl()#> # Source:   table<"public"."anon_test"> [?? x 18]#> # Database: postgres  [yourusername@localhost:/postgres]#>    granularity_time granularity_geo country_iso3 location_code border age   sex   isoyear isoweek isoyearweek season   seasonweek#>    <chr>            <chr>           <chr>        <chr>          <int> <chr> <chr>   <int>   <int> <chr>       <chr>         <dbl>#>  1 day              county          nor          county_nor03    2020 total total    2020       8 2020-08     2019/20…         31#>  2 day              county          nor          county_nor03    2020 total total    2020       8 2020-08     2019/20…         31#>  3 day              county          nor          county_nor03    2020 total total    2020       8 2020-08     2019/20…         31#>  4 day              county          nor          county_nor03    2020 total total    2020       9 2020-09     2019/20…         32#>  5 day              county          nor          county_nor03    2020 total total    2020       9 2020-09     2019/20…         32#>  6 day              county          nor          county_nor03    2020 total total    2020       9 2020-09     2019/20…         32#>  7 day              county          nor          county_nor03    2020 total total    2020       9 2020-09     2019/20…         32#>  8 day              county          nor          county_nor03    2020 total total    2020       9 2020-09     2019/20…         32#>  9 day              county          nor          county_nor03    2020 total total    2020       9 2020-09     2019/20…         32#> 10 day              county          nor          county_nor03    2020 total total    2020       9 2020-09     2019/20…         32#> # ℹ more rows#> # ℹ 6 more variables: calyear <int>, calmonth <int>, calyearmonth <chr>, date <date>, covid19_cases_testdate_n <int>,#> #   covid19_cases_testdate_pr100000 <dbl>

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