[R] devtools: improve default data import mechanism
Validation chain is now possible with checkers
Before that the expected values needed to be coherent.
Now, we can use ObjectStore to validate the input data
* add new input transformers:
- uppercase
- lowercase
* add new input checkers (raise AssertionError on error):
- decimal: take care of possible comma character as number separator
- integer: cast to int()
- yesno: to validate boolean value
- isalpha
- required: input value *must* not be empty
* new control checker:
- optional: block possible exception
we delete field in the returned dict instead of raising AssertionError
(exclusive with required)
Helper methods to manipulate indexes:
* build_rqlindex() is used to build index based on already created entities
* fetch() replace get_one()/get_many() methods by factorizing code
Minor changes in reporting:
* use tell() for all printing
* let new value for askerrors to display automatically the report (used in crontab)
# -*- coding: utf-8 -*-
"""This module provides tools to import tabular data.
:organization: Logilab
:copyright: 2001-2010 LOGILAB S.A. (Paris, FRANCE), license is LGPL v2.
:contact: http://www.logilab.fr/ -- mailto:contact@logilab.fr
:license: GNU Lesser General Public License, v2.1 - http://www.gnu.org/licenses
Example of use (run this with `cubicweb-ctl shell instance import-script.py`):
.. sourcecode:: python
from cubicweb.devtools.dataimport import *
# define data generators
GENERATORS = []
USERS = [('Prenom', 'firstname', ()),
('Nom', 'surname', ()),
('Identifiant', 'login', ()),
]
def gen_users(ctl):
for row in ctl.get_data('utilisateurs'):
entity = mk_entity(row, USERS)
entity['upassword'] = u'motdepasse'
ctl.check('login', entity['login'], None)
ctl.store.add('CWUser', entity)
email = {'address': row['email']}
ctl.store.add('EmailAddress', email)
ctl.store.relate(entity['eid'], 'use_email', email['eid'])
ctl.store.rql('SET U in_group G WHERE G name "users", U eid %(x)s', {'x':entity['eid']})
CHK = [('login', check_doubles, 'Utilisateurs Login',
'Deux utilisateurs ne devraient pas avoir le même login.'),
]
GENERATORS.append( (gen_users, CHK) )
# create controller
ctl = CWImportController(RQLObjectStore())
ctl.askerror = 1
ctl.generators = GENERATORS
ctl.store._checkpoint = checkpoint
ctl.store._rql = rql
ctl.data['utilisateurs'] = lazytable(utf8csvreader(open('users.csv')))
# run
ctl.run()
sys.exit(0)
.. BUG fichier à une colonne pose un problème de parsing
.. TODO rollback()
"""
__docformat__ = "restructuredtext en"
import sys
import csv
import traceback
import os.path as osp
from StringIO import StringIO
from logilab.common import shellutils
from logilab.common.deprecation import deprecated
def ucsvreader_pb(filepath, encoding='utf-8', separator=',', quote='"',
skipfirst=False, withpb=True):
"""same as ucsvreader but a progress bar is displayed as we iter on rows"""
if not osp.exists(filepath):
raise Exception("file doesn't exists: %s" % filepath)
rowcount = int(shellutils.Execute('wc -l "%s"' % filepath).out.strip().split()[0])
if skipfirst:
rowcount -= 1
if withpb:
pb = shellutils.ProgressBar(rowcount, 50)
for urow in ucsvreader(file(filepath), encoding, separator, quote, skipfirst):
yield urow
if withpb:
pb.update()
print ' %s rows imported' % rowcount
def ucsvreader(stream, encoding='utf-8', separator=',', quote='"',
skipfirst=False):
"""A csv reader that accepts files with any encoding and outputs unicode
strings
"""
it = iter(csv.reader(stream, delimiter=separator, quotechar=quote))
if skipfirst:
it.next()
for row in it:
yield [item.decode(encoding) for item in row]
utf8csvreader = deprecated('use ucsvreader instead')(ucsvreader)
def commit_every(nbit, store, it):
for i, x in enumerate(it):
yield x
if nbit is not None and i % nbit:
store.checkpoint()
if nbit is not None:
store.checkpoint()
def lazytable(reader):
"""The first row is taken to be the header of the table and
used to output a dict for each row of data.
>>> data = lazytable(utf8csvreader(open(filename)))
"""
header = reader.next()
for row in reader:
yield dict(zip(header, row))
def mk_entity(row, map):
"""Return a dict made from sanitized mapped values.
ValidationError can be raised on unexpected values found in checkers
>>> row = {'myname': u'dupont'}
>>> map = [('myname', u'name', (capitalize_if_unicase,))]
>>> mk_entity(row, map)
{'name': u'Dupont'}
>>> row = {'myname': u'dupont', 'optname': u''}
>>> map = [('myname', u'name', (capitalize_if_unicase,)),
... ('optname', u'MARKER', (optional,))]
>>> mk_entity(row, map)
{'name': u'Dupont'}
"""
res = {}
assert isinstance(row, dict)
assert isinstance(map, list)
for src, dest, funcs in map:
assert not (required in funcs and optional in funcs), "optional and required checks are exclusive"
res[dest] = row[src]
try:
for func in funcs:
res[dest] = func(res[dest])
if res[dest] is None or res[dest]==False:
raise AssertionError('undetermined value')
except AssertionError, err:
if optional in funcs:
# Forget this field if exception is coming from optional function
del res[dest]
else:
raise AssertionError('error with "%s" field: %s' % (src, err))
return res
# user interactions ############################################################
def tell(msg):
print msg
def confirm(question):
"""A confirm function that asks for yes/no/abort and exits on abort."""
answer = shellutils.ASK.ask(question, ('Y','n','abort'), 'Y')
if answer == 'abort':
sys.exit(1)
return answer == 'Y'
class catch_error(object):
"""Helper for @contextmanager decorator."""
def __init__(self, ctl, key='unexpected error', msg=None):
self.ctl = ctl
self.key = key
self.msg = msg
def __enter__(self):
return self
def __exit__(self, type, value, traceback):
if type is not None:
if issubclass(type, (KeyboardInterrupt, SystemExit)):
return # re-raise
if self.ctl.catcherrors:
self.ctl.record_error(self.key, None, type, value, traceback)
return True # silent
# base sanitizing functions ####################################################
def capitalize_if_unicase(txt):
if txt.isupper() or txt.islower():
return txt.capitalize()
return txt
def uppercase(txt):
return txt.upper()
def lowercase(txt):
return txt.lower()
def no_space(txt):
return txt.replace(' ','')
def no_uspace(txt):
return txt.replace(u'\xa0','')
def no_dash(txt):
return txt.replace('-','')
def decimal(value):
"""cast to float but with comma replacement
We take care of some locale format as replacing ',' by '.'"""
value = value.replace(',', '.')
try:
return float(value)
except Exception, err:
raise AssertionError(err)
def integer(value):
try:
return int(value)
except Exception, err:
raise AssertionError(err)
def strip(txt):
return txt.strip()
def yesno(value):
return value.lower()[0] in 'yo1'
def isalpha(value):
if value.isalpha():
return value
raise AssertionError("not all characters in the string alphabetic")
def optional(value):
"""validation error will not been raised if you add this checker in chain"""
return value
def required(value):
"""raise AssertionError is value is empty
This check should be often found in last position in the chain.
"""
if bool(value):
return value
raise AssertionError("required")
@deprecated('use required(value)')
def nonempty(value):
return required(value)
@deprecated('use integer(value)')
def alldigits(txt):
if txt.isdigit():
return txt
else:
return u''
# base integrity checking functions ############################################
def check_doubles(buckets):
"""Extract the keys that have more than one item in their bucket."""
return [(key, len(value)) for key,value in buckets.items() if len(value) > 1]
def check_doubles_not_none(buckets):
"""Extract the keys that have more than one item in their bucket."""
return [(key, len(value)) for key,value in buckets.items() if key is not None and len(value) > 1]
# object stores #################################################################
class ObjectStore(object):
"""Store objects in memory for *faster* validation (development mode)
But it will not enforce the constraints of the schema and hence will miss some problems
>>> store = ObjectStore()
>>> user = {'login': 'johndoe'}
>>> store.add('CWUser', user)
>>> group = {'name': 'unknown'}
>>> store.add('CWUser', group)
>>> store.relate(user['eid'], 'in_group', group['eid'])
"""
def __init__(self):
self.items = []
self.eids = {}
self.types = {}
self.relations = set()
self.indexes = {}
self._rql = None
self._checkpoint = None
def _put(self, type, item):
self.items.append(item)
return len(self.items) - 1
def add(self, type, item):
assert isinstance(item, dict), 'item is not a dict but a %s' % type(item)
eid = item['eid'] = self._put(type, item)
self.eids[eid] = item
self.types.setdefault(type, []).append(eid)
def relate(self, eid_from, rtype, eid_to):
"""Add new relation (reverse type support is available)
>>> 1,2 = eid_from, eid_to
>>> self.relate(eid_from, 'in_group', eid_to)
1, 'in_group', 2
>>> self.relate(eid_from, 'reverse_in_group', eid_to)
2, 'in_group', 1
"""
if rtype.startswith('reverse_'):
eid_from, eid_to = eid_to, eid_from
rtype = rtype[8:]
relation = eid_from, rtype, eid_to
self.relations.add(relation)
return relation
def build_index(self, name, type, func=None):
index = {}
if func is None or not callable(func):
func = lambda x: x['eid']
for eid in self.types[type]:
index.setdefault(func(self.eids[eid]), []).append(eid)
assert index, "new index '%s' cannot be empty" % name
self.indexes[name] = index
def build_rqlindex(self, name, type, key, rql, rql_params=False, func=None):
"""build an index by rql query
rql should return eid in first column
ctl.store.build_index('index_name', 'users', 'login', 'Any U WHERE U is CWUser')
"""
rset = self.rql(rql, rql_params or {})
for entity in rset.entities():
getattr(entity, key) # autopopulate entity with key attribute
self.eids[entity.eid] = dict(entity)
if entity.eid not in self.types.setdefault(type, []):
self.types[type].append(entity.eid)
assert self.types[type], "new index type '%s' cannot be empty (0 record found)" % type
# Build index with specified key
func = lambda x: x[key]
self.build_index(name, type, func)
@deprecated('get_many() deprecated. Use fetch() instead')
def get_many(self, name, key):
return self.fetch(name, key, unique=False)
@deprecated('get_one() deprecated. Use fetch(..., unique=True) instead')
def get_one(self, name, key):
return self.fetch(name, key, unique=True)
def fetch(self, name, key, unique=False, decorator=None):
"""
decorator is a callable method or an iterator of callable methods (usually a lambda function)
decorator=lambda x: x[:1] (first value is returned)
We can use validation check function available in _entity
"""
eids = self.indexes[name].get(key, [])
if decorator is not None:
if not hasattr(decorator, '__iter__'):
decorator = (decorator,)
for f in decorator:
eids = f(eids)
if unique:
assert len(eids) == 1, u'expected a single one value for key "%s" in index "%s". Got %i' % (key, name, len(eids))
eids = eids[0] # FIXME maybe it's better to keep an iterator here ?
return eids
def find(self, type, key, value):
for idx in self.types[type]:
item = self.items[idx]
if item[key] == value:
yield item
def rql(self, *args):
if self._rql is not None:
return self._rql(*args)
def checkpoint(self):
pass
class RQLObjectStore(ObjectStore):
"""ObjectStore that works with an actual RQL repository (production mode)"""
_rql = None # bw compat
def __init__(self, session=None, checkpoint=None):
ObjectStore.__init__(self)
if session is not None:
if not hasattr(session, 'set_pool'):
# connection
cnx = session
session = session.request()
session.set_pool = lambda : None
checkpoint = checkpoint or cnx.commit
self.session = session
self.checkpoint = checkpoint or session.commit
elif checkpoint is not None:
self.checkpoint = checkpoint
def rql(self, *args):
if self._rql is not None:
return self._rql(*args)
self.session.set_pool()
return self.session.execute(*args)
def create_entity(self, *args, **kwargs):
self.session.set_pool()
entity = self.session.create_entity(*args, **kwargs)
self.eids[entity.eid] = entity
self.types.setdefault(args[0], []).append(entity.eid)
return entity
def _put(self, type, item):
query = ('INSERT %s X: ' % type) + ', '.join(['X %s %%(%s)s' % (key,key) for key in item])
return self.rql(query, item)[0][0]
def relate(self, eid_from, rtype, eid_to):
# if reverse relation is found, eids are exchanged
eid_from, rtype, eid_to = super(RQLObjectStore, self).relate(eid_from, rtype, eid_to)
self.rql('SET X %s Y WHERE X eid %%(x)s, Y eid %%(y)s' % rtype,
{'x': int(eid_from), 'y': int(eid_to)}, ('x', 'y'))
# the import controller ########################################################
class CWImportController(object):
"""Controller of the data import process.
>>> ctl = CWImportController(store)
>>> ctl.generators = list_of_data_generators
>>> ctl.data = dict_of_data_tables
>>> ctl.run()
"""
def __init__(self, store, askerror=0, catcherrors=None, tell=tell,
commitevery=50):
self.store = store
self.generators = None
self.data = {}
self.errors = None
self.askerror = askerror
if catcherrors is None:
catcherrors = askerror
self.catcherrors = catcherrors
self.commitevery = commitevery # set to None to do a single commit
self._tell = tell
def check(self, type, key, value):
self._checks.setdefault(type, {}).setdefault(key, []).append(value)
def check_map(self, entity, key, map, default):
try:
entity[key] = map[entity[key]]
except KeyError:
self.check(key, entity[key], None)
entity[key] = default
def record_error(self, key, msg=None, type=None, value=None, tb=None):
tmp = StringIO()
if type is None:
traceback.print_exc(file=tmp)
else:
traceback.print_exception(type, value, tb, file=tmp)
print tmp.getvalue()
# use a list to avoid counting a <nb lines> errors instead of one
errorlog = self.errors.setdefault(key, [])
if msg is None:
errorlog.append(tmp.getvalue().splitlines())
else:
errorlog.append( (msg, tmp.getvalue().splitlines()) )
def run(self):
self.errors = {}
for func, checks in self.generators:
self._checks = {}
func_name = func.__name__[4:] # XXX
self.tell("Import '%s'..." % func_name)
try:
func(self)
except:
if self.catcherrors:
self.record_error(func_name, 'While calling %s' % func.__name__)
else:
raise
for key, func, title, help in checks:
buckets = self._checks.get(key)
if buckets:
err = func(buckets)
if err:
self.errors[title] = (help, err)
self.store.checkpoint()
nberrors = sum(len(err[1]) for err in self.errors.values())
self.tell('\nImport completed: %i entities, %i types, %i relations and %i errors'
% (len(self.store.eids), len(self.store.types),
len(self.store.relations), nberrors))
if self.errors:
if self.askerror==2 or (self.askerror and confirm('Display errors ?')):
from pprint import pformat
for errkey, error in self.errors.items():
self.tell("\n%s (%s): %d\n" % (error[0], errkey, len(error[1])))
self.tell(pformat(sorted(error[1])))
def get_data(self, key):
return self.data.get(key)
def index(self, name, key, value, unique=False):
"""create a new index
If unique is set to True, only first occurence will be kept not the following ones
"""
if unique:
try:
if value in self.store.indexes[name][key]:
return
except KeyError:
# we're sure that one is the first occurence; so continue...
pass
self.store.indexes.setdefault(name, {}).setdefault(key, []).append(value)
def tell(self, msg):
self._tell(msg)
def iter_and_commit(self, datakey):
"""iter rows, triggering commit every self.commitevery iterations"""
return commit_every(self.commitevery, self.store, self.get_data(datakey))