Managing Data Sources with srcr

Establishing the connection

Configuration files provide a simple way to represent in JSON the information needed to construct a data source. The JSON must define a single object (or hash), which is translated into a list structure within R. Two keys from the object define the database connection.

src_name

either the name of a driver function compatible with the DBI specification, such as SQLite or PostgreSQL (N.B. the initial R in the package name is not included), or the name of an old-style dplyr function used to construct a data source, typically a database connection, such as src_postgres or src_mysql.

src_args

a list, where the keys are names of arguments to the constructor, and the corresponding elements are the argument values.

Here’s a typical example:

{
    "src_name" : "Postgres",
    "src_args" : {
          "host"     : "my.database.server",
            "port"     : 5432,
            "dbname"   : "project_db",
            "username" : "my_credential",
            "password" : "DontL00k@This",
            "options"  : "-c search_path=schema0,schema1,schema2"
     },
     "post_connect_sql" : [
         "set role project_staff;"
     ],
     "post_connect_fun: [
         "function (db) {",
         "DBI::dbExecute(db, paste0('insert into connect_log (user, date) ',",
         "   'values (\'', 'my_credential', '\', \'', Sys.Date(), '\')'))",
         "set.seed(271828)",
         "message('Session setup complete')",
         "}"
     ]
}

If you’re deriving the configuration information programatically, you can pass it directly to srcr() via the config argument, but it’s perhaps more common that configuration remains the same across different connections for a given project. For these cases, {srcr} encourages separation of configuration from code.

Post-connection setup

Once the connection is established, there may be additional work to do. For example, session settings may need to be altered, or schemas to search specified, or authorization roles changed. There are two additional keys that srcr provides to address this:

post_connect_sql

This option allows you to pass a series of SQL statements to the newly-established database session for execution. In this way, you can change database session settings to match the intended use of the connection. While these statements can make any changes the database server will permit, they cannot alter the R environment directly.

post_connect_fun

This option gives you the most freedom to make changes. It lets you write an R function that takes the newly-established database connection as its single parameter. It may perform computation in the database, change connection settings, or even replace the connection. The value it returns will be passed back as the return value of srcr().

In both cases, this makes it possible to execute additional code specified in the configuration file. Since this creates the possibility that unknown code may be executed and produce unwanted effects, you need to opt in to each, using the allow_post_connect parameter to srcr().

Telling srcr() what to read directly

If you know where your configuration data lives, you can point srcr() directly to it, using the paths argument. This is a vector of paths to check, so you can provide a series of places to look, and srcr() will use the first one it finds. Each place can be a path to a local file, or a URL that returns JSON. (As an implementation detail, since srcr() uses jsonlite::fromJSON under the hood, paths can also contain a JSON string rather than a pointer to outside configuration data. We don’t make any promises about this, as jsonlite::fromJSON might change someday, but it can be a handy way to provide fallback configuration information after having srcr() check for an outside resource.)

If you just want to supply the configuration data directly, or obtain it from a source that doesn’t speak JSON, you can pass an appropriately-structured list of lists directly to srcr() via the config parameter, which overrides the search for configuration files.

Searching for configuration files

Through the find_config_files() function (implicitly called by srcr() if there’s no paths or config provided), {srcr} tries to support a number of common deployment styles through its use of default search locations for configuration files. For those who prefer per-user config files, it will look in your home directory, or, for those who like to collect you config files out of the way, in $HOME/.srcr. If you prefer to deploy configuration data with your application, you can put the configuration file in the same directory as your main application program. Finally, you can put the configuration file in the same directory as library code that calls srcr() either directly or through one intermediate call. Note that the current working directory isn’t in this search path by default; this is a measure intended to minimize the harm someone can cause by invoking your program in a working directory that might subvert the intended connection, either intentionally or through accidental use of a common configuration file name.

Similarly, srcr() will try by default to find files with the same basename as your application, or as the library file(s) making the call to srcr(). Optionally, the file can have a “type” (i.e. suffix) of .json or .conf, or none at all.

If these options don’t suit your deployment strategy, you can provide explicit hints to srcr() using the dirs, basenames, and suffices arguments.

Finally, to accommodate convention on Unix-like systems, find_config_files() first checks for a “hidden” file with a leading . before checking for the plain basename.

It’s worth noting that srcr() expects any configuration files it finds to contain JSON, regardless of the file suffix. This was done to minimize the number of other packages that are prerequisites for {srcr}. If you prefer another format, such as YAML or Apache, you can get there pretty easily (example simplified a bit):

my_srcr <- function(...) {
    files <- find_config_files(...)
    mydata <- read_my_config_format(files)
      srcr(config = mydata)
}

Using environment variables

If you need to specify where to look at runtime, you can use the environment variable BASENAME_CONFIG to point to a configuration file, where BASENAME is one of the basenames find_config_files() would usually check (see below). One note: srcr() will only pay attention to this environment variable if it points to an actual file, not a URL or JSON string. This is construed as a feature, in that it may limit the damage someone can inflict by fiddling with the environment. If you trust the environment, you can be more permissive by writing something like

my.paths <- c()
for (bn in my.basenames) {
    my.info <- Sys.getenv(paste0(toupper(bn), '_CONFIG'))
    if (my.info != '') my.paths <- c(my.paths, my.info)
}
src <- if (length(paths) > 0) srcr(paths = my.paths) else srcr(other.args)