Ligare.programming.R.process

Classes

RProcessStepBuilder([log])

Configure an object to execute an R script with Rscript.

final class Ligare.programming.R.process.RProcessStepBuilder(log=None)[source]

Configure an object to execute an R script with Rscript.

final class RProcessExecutorStepBuilder(parent, log=None)[source]

The final step in configurating an R process executor. This class can run the command with the execute() method.

__init__(parent, log=None)[source]

execute()[source]

Execute the configured R script.

Return CompletedProcess[bytes]:: The completed process object from process.run(…)
Return type:: tuple[CompletedProcess[bytes], bytes]

static execute_R_process(args, parameter_read_fd, data)[source]

Run the process specified by args, which is passed into subprocess.run as the first argument. This method adds the METHOD_ARG_READ_FD environment variable whose value is str(parameter_read_fd). This method blocks thread execution until the process completes.

Parameters:

args (list[str|bytes|PathLike[str]|PathLike[bytes]]) – The argument list to pass to subprocess.run.
parameter_read_fd (int) – A file descriptor number from which R will read method parameters.
data (bytes | None) – Data that is written to the executed process’s STDIN.

Return subprocess.CompletedProcess[bytes]:

The completed process.

Return type:

tuple[CompletedProcess[bytes], bytes]

static handle_process_errors(proc, log=None)[source]

Decode a finished process’s STDERR. If the process’s STDOUT is empty, an error is considered to have occurred, and an exception is raised. Otherwise, STDERR is logged and the function returns.

Parameters:

proc (subprocess.CompletedProcess[bytes]) – The completed process.
log (Logger) – The Logger that is written to

Raises:

Exception – Raised only if STDERR is not empty and STDOUT is empty.

Return type:

None

property method: RProcessMethodStepBuilder

property process: RProcessStepBuilder

property script: RProcessScriptStepBuilder

with_log(log)[source]

Configure the logger.

Parameters:: log (Logger)
Return Self:
Return type:: Self

final class RProcessMethodStepBuilder(parent, log=None)[source]

Configure method parameters and input for the R script to read.

__init__(parent, log=None)[source]

property script: RProcessScriptStepBuilder

with_data(data)[source]

The input data for the R script.

Parameters:: data (bytes) – The data
Return RProcessStepBuilder.RProcessExecutorStepBuilder:: The next step for configuration
Return type:: RProcessExecutorStepBuilder

with_log(log)[source]

Configure the logger.

Parameters:: log (Logger)
Return Self:
Return type:: Self

with_method_parameters(parameters)[source]

The method parameters and their values.

Parameters:: parameters (dict[str, Any]) – The parameters
Return Self:
Return type:: Self

static write_method_parameters(parameters)[source]

Open a FIFO pipe and write the dictionary parameters as a CSV to write_fd.

Parameters:: parameters (dict[str, Any]) – The parameters to write to the pipe
Return tuple[int, int]:: (read_fd, write_fd) the input/output file descriptors of the pipe
Return type:: tuple[int, int]

final class RProcessScriptStepBuilder(parent, log=None)[source]

Configure the R script to execute with Rscript.

__init__(parent, log=None)[source]

property process: RProcessStepBuilder

with_R_script_path(rscript)[source]

The path to the R script to execute with Rscript

Parameters:: rscript (_path_like) – The script path
Return RProcessStepBuilder.RProcessMethodStepBuilder:: The next step for configuration
Return type:: RProcessMethodStepBuilder

with_args(args)[source]

with_log(log)[source]

Configure the logger.

Parameters:: log (Logger)
Return Self:
Return type:: Self

__init__(log=None)[source]

with_Rscript_binary_path(rscript_path)[source]

The path to the Rscript binary.

Parameters:: rscript_path (_path_like) – The Rscript binary path
Return RProcessStepBuilder.RProcessScriptStepBuilder:: The next step for configuration
Return type:: RProcessScriptStepBuilder

with_log(log)[source]

Configure the logger.

Parameters:: log (Logger)
Return Self:
Return type:: Self