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Get site information

Source: R/getSiteInfo.R
getSiteInfo.Rd

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 named list of 20 elements of site specific information used by the application.

The first seven elements (center, baseUrl, schemaName, folderPath, queryName, lkPedColumns and mapPedColumns) are read from the configuration file when one exists. A configuration file that lacks one of these keys causes an error ("Could not find ..."). When no configuration file exists, the defaults for the ONPRC are returned instead: center "ONPRC", baseUrl "https://primeuat.ohsu.edu", schemaName "study", folderPath "/ONPRC/EHR" and queryName "demographics". A warning is signaled for the missing file only when expectConfigFile is TRUE.

The format of the configuration file is described in the notes at the top of the example file, example_nprcgenekeepr_config, in the package's extdata/examples folder.

The returned list contains the following elements.

  1. center – center name, such as "ONPRC" or "SNPRC"

  2. baseUrl – base URL of the LabKey server

  3. schemaName – LabKey schema name

  4. folderPath – LabKey folder path

  5. queryName – LabKey query name, "demographics" by default

  6. lkPedColumns – LabKey column names for the pedigree

  7. mapPedColumns – the package column names that lkPedColumns are renamed to

  8. sysname, release, version, nodename, machine, login, user and effective_user – character strings from Sys.info()

  9. homeDir and configFile – the home directory and the expected configuration file path, from getConfigFileName

  10. requiredCols – the required studbook columns, from getRequiredCols

  11. possibleCols – the possible studbook columns, from getPossibleCols

  12. includeColumns – the superset of report-inclusion columns, from getIncludeColumns

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] "6.17.0-1022-azure"
#> 
#> $version
#> [1] "#22-Ubuntu SMP Mon Jul 27 17:24:03 UTC 2026"
#> 
#> $nodename
#> [1] "runnervm8k3b6"
#> 
#> $machine
#> [1] "x86_64"
#> 
#> $login
#> [1] "unknown"
#> 
#> $user
#> [1] "runner"
#> 
#> $effective_user
#> [1] "runner"
#> 
#> $homeDir
#> [1] "/home/runner"
#> 
#> $configFile
#> [1] "/home/runner/.nprcgenekeepr_config"
#> 
#> $requiredCols
#> [1] "id"    "sire"  "dam"   "sex"   "birth"
#> 
#> $possibleCols
#>  [1] "id"           "sire"         "dam"          "sex"          "species"     
#>  [6] "gen"          "birth"        "exit"         "death"        "age"         
#> [11] "ancestry"     "population"   "origin"       "status"       "condition"   
#> [16] "departure"    "spf"          "vasxOvx"      "pedNum"       "first"       
#> [21] "second"       "first_name"   "second_name"  "recordStatus" "affected"    
#> [26] "name"        
#> 
#> $includeColumns
#>  [1] "id"          "sex"         "age"         "birth"       "exit"       
#>  [6] "population"  "condition"   "origin"      "first_name"  "second_name"
#> 
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] "6.17.0-1022-azure"
#> 
#> $version
#> [1] "#22-Ubuntu SMP Mon Jul 27 17:24:03 UTC 2026"
#> 
#> $nodename
#> [1] "runnervm8k3b6"
#> 
#> $machine
#> [1] "x86_64"
#> 
#> $login
#> [1] "unknown"
#> 
#> $user
#> [1] "runner"
#> 
#> $effective_user
#> [1] "runner"
#> 
#> $homeDir
#> [1] "/home/runner"
#> 
#> $configFile
#> [1] "/home/runner/.nprcgenekeepr_config"
#> 
#> $requiredCols
#> [1] "id"    "sire"  "dam"   "sex"   "birth"
#> 
#> $possibleCols
#>  [1] "id"           "sire"         "dam"          "sex"          "species"     
#>  [6] "gen"          "birth"        "exit"         "death"        "age"         
#> [11] "ancestry"     "population"   "origin"       "status"       "condition"   
#> [16] "departure"    "spf"          "vasxOvx"      "pedNum"       "first"       
#> [21] "second"       "first_name"   "second_name"  "recordStatus" "affected"    
#> [26] "name"        
#> 
#> $includeColumns
#>  [1] "id"          "sex"         "age"         "birth"       "exit"       
#>  [6] "population"  "condition"   "origin"      "first_name"  "second_name"
#>