Connect to the CalCOFI PostgreSQL database

Opens a DBI connection (via RPostgres) to the multi-user CalCOFI PostgreSQL database used by the CTD team for QA/QC (database calcofi, schemas ctd / work / your own). Every argument has a sensible default:

Usage

cc_pg_connect(
  dbname = "calcofi",
  host = NULL,
  port = NULL,
  user = NULL,
  password = NULL,
  tunnel = FALSE,
  ...
)

Arguments

dbname

database name; default "calcofi" ("gis" is the legacy 2022 db)

host

host name; default described above

port

port; default 5432 (PGPORT overrides; use 15432 if your tunnel maps there)

user

role name; default described above

password

password; default NULL = use ~/.pgpass

tunnel

if TRUE, start an SSH tunnel with cc_pg_tunnel() first (only meaningful off-server)

...

passed to DBI::dbConnect()

Value

a DBI connection; disconnect with DBI::dbDisconnect()

Details

• host: "postgis" when running on the CalCOFI server (RStudio Server at rstudio.calcofi.io, Shiny), otherwise "localhost" — i.e. the local end of your SSH tunnel (ssh -N calcofi, or cc_pg_tunnel()). PGHOST overrides.

• user: PGUSER if set, else the role name found in your ~/.pgpass for this host/port/database (the file you copied from the server), else your OS user name.

• password: NULL — libpq reads ~/.pgpass (Windows: %APPDATA%\\postgresql\\pgpass.conf). Pass one only for throw-away use.

See also

cc_pg_tunnel(), cc_pg_attach(), cc_get_db() for the public releases

Examples

if (FALSE) { # \dontrun{
con <- cc_pg_connect()                  # tunnel already running, ~/.pgpass in place
DBI::dbListObjects(con, DBI::Id(schema = "ctd"))
dplyr::tbl(con, I("ctd.cast"))

con <- cc_pg_connect(tunnel = TRUE)     # also opens `ssh -N calcofi` for you
} # }