Get site information

Get site information

Usage

getSiteInfo(expectConfigFile = TRUE)

Arguments

expectConfigFile

logical parameter when set to FALSE, no configuration is looked for. Default value is TRUE.

Value

A list of site specific information used by the application.

Currently this returns the following character strings in a named list.

1. {center}{One of "SNPRC" or "ONPRC"}

2. {baseUrl}{If center is "SNPRC", baseUrl is one of "https://boomer.txbiomed.local:8080/labkey" or "https://vger.txbiomed.local:8080/labkey". To allow testing, if center is "ONPRC" baseUrl is "https://boomer.txbiomed.local:8080/labkey".}

3. {schemaName}{If center is "SNPRC", schemaName is "study". If center is "ONPRC", schemaName is "study"}

4. {folderPath} {If center is "SNPRC", folderPath is "/SNPRC". If center is "ONPRC", folderPath is "/ONPRC"}

5. {queryName} {is "demographics"}

Examples

library(nprcgenekeepr)
## default sends warning if configuration file is missing
suppressWarnings(getSiteInfo())
#> $center
#> [1] "ONPRC"
#> 
#> $baseUrl
#> [1] "https://primeuat.ohsu.edu"
#> 
#> $schemaName
#> [1] "study"
#> 
#> $folderPath
#> [1] "/ONPRC/EHR"
#> 
#> $queryName
#> [1] "demographics"
#> 
#> $lkPedColumns
#> [1] "Id"              "gender"          "birth"           "death"          
#> [5] "lastDayAtCenter" "Id/parents/dam"  "Id/parents/sire"
#> 
#> $mapPedColumns
#> [1] "id"    "sex"   "birth" "death" "exit"  "dam"   "sire" 
#> 
#> $sysname
#> [1] "Linux"
#> 
#> $release
#> [1] "6.8.0-1021-azure"
#> 
#> $version
#> [1] "#25-Ubuntu SMP Wed Jan 15 20:45:09 UTC 2025"
#> 
#> $nodename
#> [1] "fv-az1657-386"
#> 
#> $machine
#> [1] "x86_64"
#> 
#> $login
#> [1] "unknown"
#> 
#> $user
#> [1] "runner"
#> 
#> $effective_user
#> [1] "runner"
#> 
#> $homeDir
#> [1] "/home/runner"
#> 
#> $configFile
#> [1] "/home/runner/.nprcgenekeepr_config"
#> 
getSiteInfo(expectConfigFile = FALSE)
#> $center
#> [1] "ONPRC"
#> 
#> $baseUrl
#> [1] "https://primeuat.ohsu.edu"
#> 
#> $schemaName
#> [1] "study"
#> 
#> $folderPath
#> [1] "/ONPRC/EHR"
#> 
#> $queryName
#> [1] "demographics"
#> 
#> $lkPedColumns
#> [1] "Id"              "gender"          "birth"           "death"          
#> [5] "lastDayAtCenter" "Id/parents/dam"  "Id/parents/sire"
#> 
#> $mapPedColumns
#> [1] "id"    "sex"   "birth" "death" "exit"  "dam"   "sire" 
#> 
#> $sysname
#> [1] "Linux"
#> 
#> $release
#> [1] "6.8.0-1021-azure"
#> 
#> $version
#> [1] "#25-Ubuntu SMP Wed Jan 15 20:45:09 UTC 2025"
#> 
#> $nodename
#> [1] "fv-az1657-386"
#> 
#> $machine
#> [1] "x86_64"
#> 
#> $login
#> [1] "unknown"
#> 
#> $user
#> [1] "runner"
#> 
#> $effective_user
#> [1] "runner"
#> 
#> $homeDir
#> [1] "/home/runner"
#> 
#> $configFile
#> [1] "/home/runner/.nprcgenekeepr_config"
#>