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rintmock filter

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rintmock


Experimental filter to run R in sections without using pexpect.

Aliases for this filter

  • rintmock

Converts from file formats:

  • .txt
  • .r
  • .R

To file formats:

  • .Rout
  • .txt

Available settings:

SettingDescriptionDefault
add-new-filesBoolean or list of extensions/patterns to match.True
added-in-versionDexy version when this filter was first available.
additional-doc-filtersFilters to apply to additional documents created as side effects.{}
additional-doc-settingsSettings to apply to additional documents created as side effects.{}
argsArguments to be passed to the executable.
check-return-codeWhether to look for nonzero return code.True
clargsArguments to be passed to the executable (same as 'args').
command-stringThe full command string.%(prog)s %(args)s "%(script_file)s" %(scriptargs)s "%(output_file)s"
data-typeAlias of custom data class to use to store filter output.sectioned
envDictionary of key-value pairs to be added to environment for runs.{}
examplesTemplates which should be used as examples for this filter.[]
exclude-add-new-filesList of patterns to skip even if they match add-new-files.[]
exclude-new-files-from-dirList of directories to skip when adding new files.[]
executableThe executable to be runR CMD BATCH --quiet --no-timing
extFile extension to output.None
extension-mapDictionary mapping input extensions to default output extensions.None
helpHelpstring for plugin.Experimental filter to run R in sections without using pexpect.
initial-timeout10
input-extensionsList of extensions which this filter can accept as input.['.txt', '.r', '.R']
keep-originalsWhether, if additional-doc-filters are specified, the original unmodified docs should also be added.False
make-dummy-outputWhether to make a dummy output file when one is not generated and add-new-files is True.False
mkdirA directory which should be created in working dir.None
mkdirsA list of directories which should be created in working dir.[]
nodocWhether filter should be excluded from documentation.False
outputWhether to output results of this filter by default by reporters such as 'output' or 'website'.False
output-extensionsList of extensions which this filter can produce as output.['.Rout', '.txt']
override-workspace-exclude-filtersIf True, document will be populated to other workspaces ignoring workspace-exclude-filters.False
path-extensionsstrings to extend path with[]
preserve-prior-data-classWhether output data class should be set to match the input data class.False
record-varsWhether to add code that will automatically record values of variables.False
require-outputShould dexy raise an exception if no output is produced by this filter?True
scriptargsArguments to be passed to the executable.
tagsTags which describe the filter.['rstats', 'repl', 'stats']
timeout10
use-wdWhether to use a custom working directory when running filter.True
variablesA dictionary of variable names and values to make available to this filter.{}
varsA dictionary of variable names and values to make available to this filter.{}
version-commandCommand to call to return version of installed software.R --version
windows-version-commandCommand to call on windows to return version of installed software.None
workspace-exclude-filtersFilters whose output should be excluded from workspace.['pyg']
workspace-includesIf set to a list of filenames or extensions, only these will be populated to working dir.None
write-stderr-to-stdoutShould stderr be piped to stdout?False
Filter Source Code
class RIntBatchSectionsFilter(SubprocessFilter):
    """
    Experimental filter to run R in sections without using pexpect.
    """
    aliases = ['rintmock']

    _settings = {
            'add-new-files' : True,
            'executable' : 'R CMD BATCH --quiet --no-timing',
            'tags' : ['rstats', 'repl', 'stats'],
            'input-extensions' : ['.txt', '.r', '.R'],
            'output-extensions' : [".Rout", '.txt'],
            'version-command' : "R --version",
            'write-stderr-to-stdout' : False,
            'data-type' : 'sectioned',
            'command-string' : """%(prog)s %(args)s "%(script_file)s" %(scriptargs)s "%(output_file)s" """
            }

    def command_string(self, section_name, section_text, wd):
        br = self.input_data.baserootname()

        args = self.default_command_string_args()
        args['script_file'] = "%s-%s%s" % (br, section_name, self.input_data.ext)
        args['output_file'] = "%s-%s-out%s" % (br, section_name, self.output_data.ext)

        work_filepath = os.path.join(wd, args['script_file'])

        with open(work_filepath, "w") as f:
            f.write(str(section_text))

        command = self.setting('command-string') %  args
        return command, args['output_file']

    def process(self):
        self.populate_workspace()
        wd = self.parent_work_dir()

        for section_name, section_text in self.input_data.items():
            command, outfile = self.command_string(section_name, section_text, wd)
            proc, stdout = self.run_command(command, self.setup_env())
            self.handle_subprocess_proc_return(command, proc.returncode, stdout)

            with open(os.path.join(wd, outfile), "r") as f:
                self.output_data[section_name] = f.read()

        if self.setting('add-new-files'):
            self.add_new_files()

        self.output_data.save()

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