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Execute a SPARQL Query with ROBOT

robot_query.Rd

Wrapper for robot("query", ...) that accepts a file or text query, and has more convenient arguments.

Usage

robot_query(
  input,
  query,
  output = NULL,
  ...,
  tidy_what = "nothing",
  col_types = NULL
)

Arguments

input

The path to an RDF/OWL file recognized by ROBOT, as a string.

query

The text for or path to a valid SPARQL query (ASK, SELECT, CONSTRUCT, or UPDATE) as a string.

output

The path where output will be written, as a string, or NULL (default) to load data directly. output is required for UPDATE and CONSTRUCT queries.

...

Additional arguments to ROBOT query formatted as described in robot().

tidy_what

The elements of a SPARQL-created data.frame to tidy, as a character vector. One or more of the following:

  • "everything" to apply all tidy operations (has precedence over "nothing").

  • "header" to remove leading ? from header labels.

  • "unnest" to unnest list columns with unnest_cross().

  • "uri_to_curie" to convert all URIs recognized by DO.utils to CURIEs with to_curie().

  • "lgl_NA_false" to replace NA in logical columns with FALSE.

  • "as_tibble" to make the output a tibble.

  • "nothing" to prevent all tidying.

col_types

One of NULL, a cols() specification, or a string. See vignette("readr") for more details.

If NULL, all column types will be inferred from guess_max rows of the input, interspersed throughout the file. This is convenient (and fast), but not robust. If the guessed types are wrong, you'll need to increase guess_max or supply the correct types yourself.

Column specifications created by list() or cols() must contain one column specification for each column. If you only want to read a subset of the columns, use cols_only().

Alternatively, you can use a compact string representation where each character represents one column:

  • c = character

  • i = integer

  • n = number

  • d = double

  • l = logical

  • f = factor

  • D = date

  • T = date time

  • t = time

  • ? = guess

  • _ or - = skip

By default, reading a file without a column specification will print a message showing what readr guessed they were. To remove this message, set show_col_types = FALSE or set `options(readr.show_col_types = FALSE).

Value

If output is specified, the path to the output file with the query result. Otherwise, the query result (ASK as boolean or SELECT as tibble).

See also

robot() for underlying implementation.