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Commit 5d2e224

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effigieseffigies
authored
Merge pull request #3291 from PennSIVE/r-interface
ENH: Interface for R
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‎nipype/interfaces/r.py

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# -*- coding: utf-8 -*-
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# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
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# vi: set ft=python sts=4 ts=4 sw=4 et:
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"""Interfaces to run R scripts."""
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import os
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from shutil import which
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from .. import config
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from .base import (
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CommandLineInputSpec,
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InputMultiPath,
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isdefined,
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CommandLine,
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traits,
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File,
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Directory,
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)
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def get_r_command():
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if "NIPYPE_NO_R" in os.environ:
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return None
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r_cmd = os.getenv("RCMD", default="R")
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return r_cmd if which(r_cmd) else None
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no_r = get_r_command() is None
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class RInputSpec(CommandLineInputSpec):
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"""Basic expected inputs to R interface"""
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script = traits.Str(
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argstr='-e "%s"', desc="R code to run", mandatory=True, position=-1
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)
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# non-commandline options
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rfile = traits.Bool(True, desc="Run R using R script", usedefault=True)
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script_file = File(
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"pyscript.R", usedefault=True, desc="Name of file to write R code to"
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)
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class RCommand(CommandLine):
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"""Interface that runs R code
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>>> import nipype.interfaces.r as r
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>>> r = r.RCommand(rfile=False) # doctest: +SKIP
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>>> r.inputs.script = "Sys.getenv('USER')" # doctest: +SKIP
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>>> out = r.run() # doctest: +SKIP
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"""
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_cmd = get_r_command()
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input_spec = RInputSpec
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def __init__(self, r_cmd=None, **inputs):
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"""initializes interface to r
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(default 'R')
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"""
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super(RCommand, self).__init__(**inputs)
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if r_cmd and isdefined(r_cmd):
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self._cmd = r_cmd
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# For r commands force all output to be returned since r
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# does not have a clean way of notifying an error
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self.terminal_output = "allatonce"
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def set_default_r_cmd(self, r_cmd):
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"""Set the default R command line for R classes.
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This method is used to set values for all R
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subclasses.
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"""
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self._cmd = r_cmd
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def set_default_rfile(self, rfile):
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"""Set the default R script file format for R classes.
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This method is used to set values for all R
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subclasses.
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"""
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self._rfile = rfile
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def _run_interface(self, runtime):
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self.terminal_output = "allatonce"
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runtime = super(RCommand, self)._run_interface(runtime)
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if "R code threw an exception" in runtime.stderr:
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self.raise_exception(runtime)
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return runtime
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def _format_arg(self, name, trait_spec, value):
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if name in ["script"]:
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argstr = trait_spec.argstr
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return self._gen_r_command(argstr, value)
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return super(RCommand, self)._format_arg(name, trait_spec, value)
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def _gen_r_command(self, argstr, script_lines):
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"""Generates commands and, if rfile specified, writes it to disk."""
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if not self.inputs.rfile:
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# replace newlines with ;, strip comments
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script = "; ".join(
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[
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line
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for line in script_lines.split("\n")
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if not line.strip().startswith("#")
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]
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)
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# escape " and $
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script = script.replace('"', '\\"')
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script = script.replace("$", "\\$")
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else:
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script_path = os.path.join(os.getcwd(), self.inputs.script_file)
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with open(script_path, "wt") as rfile:
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rfile.write(script_lines)
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script = "source('%s')" % script_path
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return argstr % script

‎nipype/interfaces/tests/test_auto_RCommand.py

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# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
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from ..r import RCommand
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def test_RCommand_inputs():
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input_map = dict(
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args=dict(
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argstr="%s",
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),
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environ=dict(
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nohash=True,
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usedefault=True,
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),
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rfile=dict(
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usedefault=True,
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),
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script=dict(
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argstr='-e "%s"',
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mandatory=True,
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position=-1,
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),
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script_file=dict(
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extensions=None,
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usedefault=True,
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),
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)
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inputs = RCommand.input_spec()
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for key, metadata in list(input_map.items()):
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for metakey, value in list(metadata.items()):
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assert getattr(inputs.traits()[key], metakey) == value

‎nipype/interfaces/tests/test_r.py

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# -*- coding: utf-8 -*-
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# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
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# vi: set ft=python sts=4 ts=4 sw=4 et:
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import os
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import pytest
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from nipype.interfaces import r
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no_r = r.no_r
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@pytest.mark.skipif(no_r, reason="R is not available")
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def test_cmdline(tmp_path):
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default_script_file = str(tmp_path / "testscript")
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ri = r.RCommand(script="1 + 1", script_file=default_script_file, rfile=False)
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r_cmd = r.get_r_command()
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assert ri.cmdline == r_cmd + (' -e "1 + 1"')
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assert ri.inputs.script == "1 + 1"
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assert ri.inputs.script_file == default_script_file
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assert not os.path.exists(ri.inputs.script_file), "scriptfile should not exist"
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assert not os.path.exists(
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default_script_file
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), "default scriptfile should not exist."
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@pytest.mark.skipif(no_r, reason="R is not available")
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def test_run_interface(tmpdir):
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cwd = tmpdir.chdir()
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default_script_file = r.RInputSpec().script_file
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rc = r.RCommand(r_cmd="foo_m")
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assert not os.path.exists(default_script_file), "scriptfile should not exist 1."
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with pytest.raises(ValueError):
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rc.run() # script is mandatory
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assert not os.path.exists(default_script_file), "scriptfile should not exist 2."
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if os.path.exists(default_script_file): # cleanup
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os.remove(default_script_file)
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rc.inputs.script = "a=1;"
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assert not os.path.exists(default_script_file), "scriptfile should not exist 3."
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with pytest.raises(IOError):
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rc.run() # foo_m is not an executable
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assert os.path.exists(default_script_file), "scriptfile should exist 3."
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if os.path.exists(default_script_file): # cleanup
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os.remove(default_script_file)
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cwd.chdir()
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@pytest.mark.skipif(no_r, reason="R is not available")
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def test_set_rcmd(tmpdir):
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cwd = tmpdir.chdir()
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default_script_file = r.RInputSpec().script_file
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ri = r.RCommand()
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_default_r_cmd = ri._cmd
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ri.set_default_r_cmd("foo")
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assert not os.path.exists(default_script_file), "scriptfile should not exist."
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assert ri._cmd == "foo"
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ri.set_default_r_cmd(_default_r_cmd)
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cwd.chdir()

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