Source code for

R help system.

import os
from collections import namedtuple
import re
import sqlite3
import typing
import warnings

import rpy2.rinterface as rinterface
from rpy2.rinterface import StrSexpVector

from rpy2.robjects.packages_utils import (get_packagepath,
from collections import OrderedDict

tmp = rinterface.baseenv['R.Version']()
tmp_major = int(tmp[tmp.do_slot('names').index('major')][0])
tmp_minor = float(tmp[tmp.do_slot('names').index('minor')][0])
readRDS = rinterface.baseenv['readRDS']

del tmp
del tmp_major
del tmp_minor

_eval = rinterface.baseenv['eval']

NON_UNIQUE_TAGS = set((r'\alias', r'\keyword', r'\section'))

def quiet_require(name: str, lib_loc: typing.Optional[str] = None) -> bool:
    """ Load an R package /quietly/ (suppressing messages to the console). """
    if lib_loc is None:
        lib_loc = "NULL"
    expr_txt = ('suppressPackageStartupMessages(base::require(%s, lib.loc=%s))'
                % (name, lib_loc))
    expr = rinterface.parse(expr_txt)
    ok = _eval(expr)
    return ok

_get_namespace = rinterface.baseenv['getNamespace']
_lazyload_dbfetch = rinterface.baseenv['lazyLoadDBfetch']

tools_ns = _get_namespace(StrSexpVector(('tools',)))
_Rd_db = tools_ns['Rd_db']
_Rd_deparse = tools_ns['.Rd_deparse']

__rd_meta = os.path.join('Meta', 'Rd.rds')
__package_meta = os.path.join('Meta', 'package.rds')

p_newarg = re.compile(r'^\s*([a-zA-Z\._][a-zA-Z0-9\._]*?)\s*:\s*(.+?)\s*$')
p_desc = re.compile(r'^\s+([^\s]+.*?)\s*$')

def _Rd2txt(section_doc):
    tempfilename = rinterface.baseenv['tempfile']()[0]
    filecon = rinterface.baseenv['file'](tempfilename, open='w')
            section_doc, out=filecon, fragment=True
        with open(tempfilename) as fh:
            section_rows = fh.readlines()
    return section_rows

def create_metaRd_db(dbcon) -> None:
    """ Create an database to store R help pages.

    dbcon: database connection (assumed to be SQLite - may or may not work
           with other databases)
CREATE TABLE package (
title TEXT,
version TEXT,
description TEXT
CREATE TABLE rd_meta (
id INTEGER, file TEXT UNIQUE, name TEXT, type TEXT, title TEXT, encoding TEXT,
package_rowid INTEGER
CREATE INDEX type_idx ON rd_meta (type);
CREATE TABLE rd_alias_meta (
rd_meta_rowid INTEGER, alias TEXT
CREATE INDEX alias_idx ON rd_alias_meta (alias);

def populate_metaRd_db(package_name: str, dbcon,
                       package_path: typing.Optional[str] = None) -> None:
    """ Populate a database with the meta-information
    associated with an R package: version, description, title, and
    aliases (those are what the R help system is organised around).

    - package_name: a string
    - dbcon: a database connection
    - package_path: path the R package installation (default: None)
    if package_path is None:
        package_path = get_packagepath(package_name)

    rpath = StrSexpVector((os.path.join(package_path,

    rds = readRDS(rpath)
    desc = rds[rds.do_slot('names').index('DESCRIPTION')]
    db_res = dbcon.execute('insert into package values (?,?,?,?)',
    package_rowid = db_res.lastrowid

    rpath = StrSexpVector((os.path.join(package_path,

    rds = readRDS(rpath)
    FILE_I = rds.do_slot("names").index('File')
    NAME_I = rds.do_slot("names").index('Name')
    TYPE_I = rds.do_slot("names").index('Type')
    TITLE_I = rds.do_slot("names").index('Title')
    ENCODING_I = rds.do_slot("names").index('Encoding')
    ALIAS_I = rds.do_slot("names").index('Aliases')
    for row_i in range(len(rds[0])):
        db_res = dbcon.execute('insert into rd_meta values (?,?,?,?,?,?,?)',
        rd_rowid = db_res.lastrowid
        for alias in rds[ALIAS_I][row_i]:
            dbcon.execute('insert into rd_alias_meta values (?,?)',
                          (rd_rowid, alias))

Item = namedtuple('Item', 'name value')

[docs] class Page(object): """ An R documentation page. The original R structure is a nested sequence of components, corresponding to the latex-like .Rd file An help page is divided into sections, the names for the sections are the keys for the dict attribute 'sections', and a given section can be extracted with the square-bracket operator. In R, the S3 class 'Rd' is the closest entity to this class. """ def __init__(self, struct_rdb: rinterface.ListSexpVector, _type: str = ''): sections = OrderedDict() for elt_i in range(len(struct_rdb)): elt = rinterface.baseenv['['](struct_rdb, elt_i+1) rd_tag = elt[0].do_slot("Rd_tag")[0] if rd_tag in sections and rd_tag not in NON_UNIQUE_TAGS: warnings.warn('Section of the R doc duplicated: %s' % rd_tag) sections[rd_tag] = elt self._sections = sections self._type = _type def _section_get(self): return self._sections sections = property(_section_get, None, None, 'Sections in the in help page, as a dict.') def __getitem__(self, item): """ Get a section """ return self.sections[item]
[docs] def arguments(self) -> typing.List[Item]: """ Get the arguments and descriptions as a list of Item objects. """ section_doc = self._sections.get(r'\arguments') res: typing.List[Item] = list() if section_doc is None: return res else: arg_name = None arg_desc = None section_rows = _Rd2txt(section_doc) if len(section_rows) < 3: return res for row in section_rows[2:]: if arg_name is None: m = p_newarg.match(row) if m: arg_name = m.groups()[0] arg_desc = [m.groups()[1]] else: if p_desc.match(row): arg_desc.append(row.strip()) else: res.append( Item(arg_name, arg_desc) ) arg_name = None arg_desc = None if arg_name is not None: res.append( Item(arg_name, arg_desc) ) return res
def _get_section(self, section: str): section_doc = self._sections.get(section, None) if section_doc is None: res = '' else: res = _Rd2txt(section_doc) return res
[docs] def description(self) -> str: """ Get the description of the entry """ return self._get_section(r'\description')
[docs] def details(self) -> str: """ Get the section Details for the documentation entry.""" return self._get_section(r'\details')
[docs] def title(self) -> str: """ Get the title """ return self._get_section(r'\title')
[docs] def value(self) -> str: """ Get the value returned """ return self._get_section(r'\value')
[docs] def seealso(self) -> str: """ Get the other documentation entries recommended """ return self._get_section(r'\seealso')
[docs] def usage(self) -> str: """ Get the usage for the object """ return self._get_section(r'\usage')
[docs] def items(self): """ iterator through the sections names and content in the documentation Page. """ return self.sections.items()
[docs] def iteritems(self): """ iterator through the sections names and content in the documentation Page. (deprecated, use items()) """ warnings.warn('Use the method items().', DeprecationWarning) return self.sections.items()
[docs] def to_docstring( self, section_names: typing.Optional[typing.Tuple[str, ...]] = None ) -> str: """ section_names: list of section names to consider. If None all sections are used. Returns a string that can be used as a Python docstring. """ s = [] if section_names is None: section_names = self.sections.keys() def walk(tree): if not isinstance(tree, str): for elt in tree: walk(elt) else: s.append(tree) s.append(' ') for name in section_names: name_str = name[1:] if name.startswith('\\') else name s.append(name_str) s.append(os.linesep) s.append('-' * len(name_str)) s.append(os.linesep) s.append(os.linesep) walk(self.sections[name]) s.append(os.linesep) s.append(os.linesep) return ''.join(s)
[docs] class Package(object): """ The R documentation page (aka help) for a package. """ __package_path = None __package_name = None __aliases_info = 'aliases.rds' __hsearch_meta = os.path.join('Meta', 'hsearch.rds') __paths_info = 'paths.rds' __anindex_info = 'AnIndex' def __package_name_get(self): return self.__package_name name = property(__package_name_get, None, None, 'Name of the package as known by R') def __init__(self, package_name: str, package_path: typing.Optional[str] = None): self.__package_name = package_name if package_path is None: package_path = get_packagepath(package_name) self.__package_path = package_path rd_meta_dbcon = sqlite3.connect(':memory:') create_metaRd_db(rd_meta_dbcon) populate_metaRd_db(package_name, rd_meta_dbcon, package_path=package_path) self._dbcon = rd_meta_dbcon path = os.path.join(package_path, 'help', package_name + '.rdx') self._rdx = readRDS(StrSexpVector((path, )))
[docs] def fetch(self, alias: str) -> Page: """ Fetch the documentation page associated with a given alias. For S4 classes, the class name is *often* suffixed with '-class'. For example, the alias to the documentation for the class AnnotatedDataFrame in the package Biobase is 'AnnotatedDataFrame-class'. """ c = self._dbcon.execute( 'SELECT rd_meta_rowid, alias FROM rd_alias_meta WHERE alias=?', (alias, ) ) res_alias = c.fetchall() if len(res_alias) == 0: raise HelpNotFoundError( 'No help could be fetched', topic=alias, package=self.__package_name ) c = self._dbcon.execute( 'SELECT file, name, type FROM rd_meta WHERE rowid=?', (res_alias[0][0], ) ) # since the selection is on a verified rowid we are sure to # exactly get one row res_all = c.fetchall() rkey = StrSexpVector((res_all[0][0][:-3], )) _type = res_all[0][2] rpath = StrSexpVector( (os.path.join(self.package_path, 'help', f'{self.__package_name}.rdb'),) ) rdx_variables = ( self._rdx[self._rdx.do_slot('names').index('variables')] ) _eval = rinterface.baseenv['eval'] devnull_func = rinterface.parse('function(x) {}') devnull_func = _eval(devnull_func) res = _lazyload_dbfetch( rdx_variables[rdx_variables.do_slot('names').index(rkey[0])], rpath, self._rdx[self._rdx.do_slot('names').index("compressed")], devnull_func ) p_res = Page(res, _type=_type) return p_res
package_path = property(lambda self: str(self.__package_path), None, None, 'Path to the installed R package') def __repr__(self): r = 'R package %s %s' % (self.__package_name, super(Package, self).__repr__()) return r
class HelpNotFoundError(KeyError): """ Exception raised when an help topic cannot be found. """ def __init__(self, msg, topic=None, package=None): super(HelpNotFoundError, self).__init__(msg) self.topic = topic self.package = package
[docs] def pages(topic): """ Get help pages corresponding to a given topic. """ res = list() for path in _libpaths(): for name in _packages(**{'all.available': True, 'lib.loc': StrSexpVector((path,))}): # TODO: what if the same package is installed # at different locations ? pack = Package(name) try: page = pack.fetch(topic) res.append(page) except HelpNotFoundError: pass return tuple(res)
def docstring( package: Package, alias: str, sections: typing.Tuple[str, ...] = (r'\usage', r'\arguments')) -> str: """Fetch the R documentation for an alias in a package.""" if not isinstance(package, Package): package = Package(package) page = package.fetch(alias) return page.to_docstring(sections)