def render(self):
try:
getValidationErrors(interfaces.IBiblatexEntry, self.context)
except Exception:
return u'<span class="error schema-validation-error">S</span>'
else:
return u''
def __init__(self, context):
logging.Filter.__init__(self)
errs = getValidationErrors(ICheckContext, context)
if errs:
raise ValueError('Not a proper context: %r' %(errs))
self.context = context
def verify(self):
errors = schema.getValidationErrors(
[a for a in
implementedBy(self.__class__)][0],
self)
if errors:
raise schema.ValidationError(errors)
def test_historyevent_invariant(self):
"""
Exercise the different validation options fo HistoryEvent Objects.
"""
# Duration events with no end date are invalid
hevent = HistoryEvent()
hevent.title = u"95th World Congress of Esperanto"
hevent.durationEvent = True
hevent.start = u"Jul 17 2010 00:00:00 GMT-0600"
errors = schema.getValidationErrors(IHistoryEvent, hevent)
self.assertGreater(len(errors), 0)
# adding the missing piece of data makes the validator happy
hevent.end = u"JFeb 11 2012 00:00:00 GMT-0600"
errors = schema.getValidationErrors(IHistoryEvent, hevent)
self.assertEqual(len(errors), 0)
def test_instance_conforms_to_IPermission(self):
from zope.interface.verify import verifyObject
from zope.security.interfaces import IPermission
from zope.schema import getValidationErrors
verifyObject(IPermission, self._makeOne('testing'))
self.assertEqual([],
getValidationErrors(IPermission,
self._makeOne('testing')))
def test_classification_edit_acceptable(self):
second_classification_folder = api.content.create(
container=self.parent,
type="ClassificationFolder",
id="classification_folder_2",
title=u"Folder 2",
classification_categories=[self.category.UID()],
internal_reference_no=u"future acceptable",
)
errors = getValidationErrors(IClassificationFolder,
second_classification_folder)
self.assertEquals(len(errors), 0)
second_classification_folder.internal_reference_no = u"still acceptable"
errors = getValidationErrors(IClassificationFolder,
second_classification_folder)
self.assertEquals(len(errors), 0)
def _validatePrincipal(self, principal):
from zope.security.interfaces import IPrincipal
from zope.interface.verify import verifyObject
from zope.schema import getValidationErrors
self.assertTrue(verifyObject(IPrincipal, principal))
errors = getValidationErrors(IPrincipal, principal)
self.assertEqual([], errors)
def test_interfaces__IField__2(field):
"""Using the `choice` type requires values to be added."""
field.type = u'Choice'
errors = getValidationErrors(IField, field)
assert 1 == len(errors)
assert errors[0][0] is None
assert isinstance(errors[0][1], Invalid)
assert ((u'type "choice" requires at least one field value.',
) == errors[0][1].args)
def create(cls, gc, **kwargs):
factory = namedtuple('Configuration', kwargs.keys())
configuration = factory(**kwargs)
if cls.check_configuration is not None:
errors = []
for iface in cls.check_configuration:
errors.extends(getValidationErrors(iface, configuration))
if errors:
raise RuntimeError('Errors occured: %s' % ', '.join(errors))
return cls(configuration)
def isValid(self):
"""Check if the response is valid.
Meaning: a response has been filled in.
"""
errors = schema.getValidationErrors(IIssue, self)
if errors:
return False
else:
return True
def push_data(self):
data = self.request.get('json', '[]')
data_list = json.loads(data)
names = getFieldNamesInOrder(IAnalysisResults)
names.remove('uuid')
names.remove('sample_no')
success_count = 0
for entry in data_list:
return_obj = ReturnData()
[setattr(return_obj, key, entry[key]) for key in entry]
errors = schema.getValidationErrors(IAnalysisResults, return_obj)
if errors:
msg = []
for error in errors:
error_type = error[1].__class__.__name__
field_value = unicode(error[1])
err = u'{0}: {1}; '.format(error_type, field_value)
msg.append(err)
msg = ''.join(msg)
entry.update(dict(_back_success=False, _back_message=msg))
logger.warn(msg)
continue
else:
uuid = entry['uuid']
obj = api.content.uuidToObject(uuid)
if obj:
[setattr(obj, k, entry[k]) for k in entry if k in names]
old_steps = obj.steps
new_steps = u'step5'
obj.steps = new_steps
notify(StepsChangedEvent(obj, old_steps, new_steps))
modified(obj)
try:
api.content.transition(obj=obj, transition='submit')
except (MissingParameterError,
InvalidParameterError) as error:
msg = 'Warning, {0}'.format(str(error))
logger.warn(error)
else:
msg = 'Success.'
success_count += 1
entry.update(dict(_back_success=True, _back_message=msg))
else:
msg = u'Warning, ' \
u'uuid "{0}" not found, skipping.'.format(uuid)
entry.update(dict(_back_success=False, _back_message=msg))
logger.warn(msg)
failed_count = len(data_list) - success_count
msg = u'Analysis of Results: {0} Item Succeeded, ' \
u'{1} Item Failed.'.format(success_count, failed_count)
logger.info(msg)
return json.dumps(data_list)
def test_valid(self):
from zope.interface.verify import verifyObject
from zope.schema import getValidationErrors
schema = self._getTargetInterface()
group = self._getTargetClass()("id", "title", "desc")
self.assertTrue(verifyObject(schema, group))
errors = getValidationErrors(schema, group)
self.assertEqual([], errors)
def isValid(self):
"""Check if the response is valid.
Meaning: a response has been filled in.
"""
errors = schema.getValidationErrors(IIssue, self)
if errors:
return False
else:
return True
def validate_attribute_values(schema, values):
obj = namedtuple('ImportObject', values.keys())(**values)
for error in getValidationErrors(schema, obj):
column = schema[error[0]].title
if isinstance(error[1], (SchemaNotFullyImplemented, RequiredMissing)):
raise ContentImportError(
_(u'Required column is missing'), colname=column
)
else:
raise ContentImportError(error, colname=column)
def _extract_metadata(context, action):
gsm = component.getGlobalSiteManager()
# is this the right way to fetch the registered Interface ?
interfaces = [interface for interfaceName, interface in
gsm.getUtilitiesFor(IMetadata)]
metadataInterface = interfaces[0]
metadata = component.getAdapter(context, metadataInterface, name=action)
errors = schema.getValidationErrors(IMetadata, metadata)
if errors:
raise interface.Invalid(errors)
payload = serialize(metadataInterface, metadata)
return payload
def _validate_after_update(self, iface, ext_self):
errors = schema.getValidationErrors(iface, ext_self)
if errors:
__traceback_info__ = errors
try:
raise errors[0][1]
except SchemaNotProvided as e: # pragma: no cover
# XXX: We shouldn't be able to get here;
# ext_setattr should be doing this
# This can probably be removed
if not e.args: # zope.schema doesn't fill in the details, which sucks
e.args = (errors[0][0], )
raise
def test_zcml_valid(self):
from zope.configuration import xmlconfig
import zope.security
from zope.interface.verify import verifyObject
from zope.security.interfaces import IPermission
from zope.schema import getValidationErrors
xmlconfig.file('configure.zcml', zope.security)
vocabulary = self._callFUT()
vocabulary = sorted(vocabulary, key=lambda term: term.token)
self.assertEqual(6, len(vocabulary))
for term in vocabulary:
p = term.value
__traceback_info__ = term.token, p
verifyObject(IPermission, p)
self.assertEqual([], getValidationErrors(IPermission, p))
def describe_mismatch(self, item, mismatch_description):
x = None
md = mismatch_description
md.append_text(str(type(item)))
errors = getValidationErrors(self.iface, item)
for attr, exc in errors:
try:
raise exc
except ValidationError:
md.append_text(' has attribute "')
md.append_text(attr)
md.append_text('" with error "')
md.append_text(repr(exc))
md.append_text('"\n\t ')
except Invalid as x: # pragma: no cover
md.append_text(str(x).replace('\n', ''))
def process_action(self, environ, datacls):
params = self.extract(environ)
fields = list(extract_fields(self.fields, params))
data = datacls(*fields)
errors = getValidationErrors(self.iface, data)
nb_errors = len(errors)
if nb_errors:
summary = {}
for field, error in errors:
doc = getattr(error, 'doc', error.__str__)
field_errors = summary.setdefault(field, [])
field_errors.append(doc())
return reply(400,
text=json.dumps(summary),
content_type="application/json")
return data
def validate(self, data, **kw):
pdb = kw.get('pdb', None)
cdata = self.to_event_values(data, pdb=pdb)
obj = Dummy(**cdata)
alsoProvides(obj , i.ILiberticEventMapping)
def filtered(value):
ret = False
fn, ferror = value
if fn in not_settable:
ret = True
if not i.ILiberticEventMapping[fn].required and isinstance(ferror, SchemaNotFullyImplemented):
ret = True
return ret
errors = [a for a in
schema.getValidationErrors(i.ILiberticEventMapping, obj)
if not filtered(a) ]
if errors:
raise schema.ValidationError(errors)
return cdata
def _callFUT(self, schema, object):
from zope.schema import getValidationErrors
return getValidationErrors(schema, object)
def import_data(self, import_step=u'step1'):
simulation_mode = self.request.form.get('form.widgets.simulation')
self.request.form['form.widgets.simulation'] = simulation_mode
if simulation_mode:
msg = _(u'Dry run mode')
api.portal.show_message(msg, self.request, 'info')
all_true_mode = self.request.form.get('form.widgets.all_true')
self.request.form['form.widgets.all_true'] = all_true_mode
if all_true_mode:
msg = _(u'Force all success')
api.portal.show_message(msg, self.request, 'info')
upload_file = self.request.form.get('form.widgets.excelFile', None)
if upload_file is None or not upload_file.filename:
msg = _(u'No files were selected.')
api.portal.show_message(msg, self.request, 'warn')
return self.index()
self.request['form.widgets.filename'] = upload_file.filename
steps_schema = (
IBloodSample,
INAExtraction,
ILibraryConstruction,
IComputerDetecting,
IAnalysisResults,
)
valid_steps = (
u'step1',
u'step2',
u'step3',
u'step4',
u'step5',
)
query_param = (
{},
{
'portal_type': 'Tumour',
'steps': u'step1',
'sort_on': 'modified',
'sort_order': 'descending'
},
{
'portal_type': 'Tumour',
'steps': u'step2',
'sort_on': 'modified',
'sort_order': 'descending'
},
{
'portal_type': 'Tumour',
'steps': u'step3',
'sort_on': 'modified',
'sort_order': 'descending'
},
{
'portal_type': 'Tumour',
'steps': u'step4',
'sort_on': 'modified',
'sort_order': 'descending'
},
{
'portal_type': 'Tumour',
'sort_on': 'modified',
'sort_order': 'descending'
},
)
step_index = valid_steps.index(import_step)
step_schema = steps_schema[step_index]
start, end = utils.steps_start_end[step_index]
query_type = {
'portal_type': 'Tumour',
'sort_on': 'modified',
'sort_order': 'descending'
}
query_type_steps = query_param[step_index]
try:
workbook = open_workbook(file_contents=upload_file.read())
except Exception:
msg = _(u'File type not supported.')
api.portal.show_message(msg, self.request, 'error')
return self.index()
sheet = workbook.sheet_by_index(0)
data_cols = utils.import_len
if sheet.ncols != data_cols:
msg = translate(_(
u'Excel data format error. '
u'Please correct it and retry. '
u'Error: expected ${expected} - got ${got}.',
mapping={
'expected': data_cols,
'got': sheet.ncols
}),
context=self.request)
api.portal.show_message(msg, self.request, 'error')
return self.index()
fields_name = utils.fields_name()
fields_title = utils.fields_title()
step_fields = utils.fields()[start:end]
step_fields_name = fields_name[start:end]
feedback_title = [
_(u'Success or failure'),
_(u'Line number'),
_(u'Execution results')
] + fields_title[start:end]
generator = getUtility(IUUIDGenerator)
gid = generator()
feedback_row = []
success_count = 0
starttime = datetime.now()
msg = 'Start importing {0} tumour objects at {1}'.format(
sheet.nrows - 2, starttime)
logger.info(msg)
sample_title = fields_title[0]
sample_no_unique = []
for row_index in range(2, sheet.nrows):
row_value = sheet.row_values(row_index)
sample_value = row_value[0]
step_value = row_value[start:end]
row_buffer = [logging.NOTSET, row_index + 1, '']
step_obj = DummyStep()
for index, field in enumerate(step_fields):
if not step_value[index]:
step_value[index] = None
elif field[1].__class__ is schema.Date:
try:
date_value = xldate_as_tuple(step_value[index],
workbook.datemode)
step_value[index] = date(*date_value[:3])
except (ValueError, TypeError):
row_buffer[0] = logging.ERROR
elif field[1].__class__ is schema.Datetime:
try:
date_value = xldate_as_tuple(step_value[index],
workbook.datemode)
step_value[index] = datetime(*date_value[:6])
except (ValueError, TypeError):
row_buffer[0] = logging.ERROR
elif field[1].__class__ is schema.Int:
try:
step_value[index] = int(step_value[index])
except (ValueError, TypeError):
row_buffer[0] = logging.ERROR
elif field[1].__class__ is schema.Float:
try:
step_value[index] = float(step_value[index])
except (ValueError, TypeError):
row_buffer[0] = logging.ERROR
elif field[1].__class__ is schema.URI:
try:
step_value[index] = str(step_value[index])
except (ValueError, TypeError):
row_buffer[0] = logging.ERROR
elif field[1].__class__ is schema.Choice:
if field[0] == 'result':
title_value_mapping = invert_result_local
value = unicode(step_value[index])
if value in title_value_mapping:
step_value[index] = title_value_mapping[value]
else:
step_value[index] = value
elif field[1].__class__ is schema.List:
if field[0] == 'treatment_situation':
title_value_mapping = invert_situation_local
elif field[0] == 'na_extraction_type':
title_value_mapping = invert_na_types_local
value = unicode(step_value[index]).split(',')
step_value[index] = []
for item in value:
if item in title_value_mapping:
step_value[index].append(title_value_mapping[item])
else:
step_value[index].append(item)
elif field[1].__class__.__name__ in ('NamedBlobImage',
'NamedBlobFile'):
try:
step_value[index] = str(step_value[index]).strip()
except (ValueError, TypeError):
row_buffer[0] = logging.ERROR
else:
value = step_value[index]
if isinstance(value, float) and value - int(value) == 0.0:
step_value[index] = int(value)
step_value[index] = unicode(step_value[index]).strip()
setattr(step_obj, field[0], step_value[index])
value = sample_value
if isinstance(value, float) and value - int(value) == 0.0:
sample_value = int(value)
sample_value = unicode(sample_value).strip()
setattr(step_obj, 'sample_no', sample_value)
errors = schema.getValidationErrors(step_schema, step_obj)
if errors:
self.extract_error(errors, row_buffer, step_schema)
if sample_value in sample_no_unique:
msg = translate(_(
u'ValuesError: '
u'${sample_title} ${sample_value} are not unique; ',
mapping={
'sample_title': sample_title,
'sample_value': sample_value
}),
context=self.request)
row_buffer[0] = logging.ERROR
row_buffer[2] += msg
else:
sample_no_unique.append(sample_value)
row_buffer += step_value
if row_buffer[0] == logging.ERROR:
feedback_row.append(row_buffer)
continue
brains_sample = api.content.find(
**merge_two_dicts(query_type, {'sample_no': sample_value}))
if import_step == valid_steps[0]:
if brains_sample:
msg = translate(_(
u'ValuesError: '
u'${sample_title} ${sample_value} already exist; ',
mapping={
'sample_title': sample_title,
'sample_value': sample_value
}),
context=self.request)
row_buffer[0] = logging.ERROR
row_buffer[2] += msg
feedback_row.append(row_buffer)
continue
validate_obj = step_obj
invariant_errors = []
try:
ITumour.validateInvariants(validate_obj, invariant_errors)
except zope.interface.exceptions.Invalid:
pass
except AttributeError:
pass
errors = [(None, e) for e in invariant_errors]
invalid = False
for error in errors:
if error[0] is None:
msg = error[1].args[0]
msg = translate(_(msg), context=self.request)
row_buffer[2] += msg
invalid = True
if invalid:
row_buffer[0] = logging.ERROR
feedback_row.append(row_buffer)
continue
if simulation_mode:
obj = step_obj
obj.gid = gid
else:
today = datetime.today()
year, month, day = today.year, today.month, today.day
container = make_folder(self.aq_parent, (year, month, day))
obj = createContentInContainer(container,
portal_type='Tumour')
map(lambda k, v: setattr(obj, k, v), step_fields_name,
step_value)
obj.steps = import_step
obj.title = unicode(sample_value)
obj.gid = gid
modified(obj)
msg = translate(_(
u"Import successful: "
u"${sample_title} ${sample_value}; ",
mapping={
'sample_title': sample_title,
'sample_value': sample_value
}),
context=self.request)
if row_buffer[0] < logging.INFO:
row_buffer[0] = logging.INFO
row_buffer[2] += msg
feedback_row.append(row_buffer)
elif import_step in valid_steps:
if not brains_sample:
msg = translate(_(
u"ValuesError: "
u"${sample_title} ${sample_value} does't exist; ",
mapping={
'sample_title': sample_title,
'sample_value': sample_value
}),
context=self.request)
row_buffer[0] = logging.ERROR
row_buffer[2] += msg
feedback_row.append(row_buffer)
continue
brains_steps = api.content.find(**merge_two_dicts(
query_type_steps, {'sample_no': sample_value}))
if not brains_steps:
expected_steps = translate(_(query_type_steps['steps']),
context=self.request)
got_steps = translate(_(brains_sample[0].steps),
context=self.request)
msg = translate(_(
u'StepsError: '
u'steps expected ${expected}, got ${got}; ',
mapping={
'expected': expected_steps,
'got': got_steps
}),
context=self.request)
row_buffer[0] = logging.ERROR
row_buffer[2] += msg
feedback_row.append(row_buffer)
continue
validate_obj = brains_sample[0].getObject()
invalid = False
for the_field, the_value in zip(step_fields, step_value):
field_type = the_field[1].__class__.__name__
field_name = the_field[0]
if field_type in ('NamedBlobImage', 'NamedBlobFile'):
if not simulation_mode and the_value != '':
success = self.fetch_data(the_field, the_value,
validate_obj, row_buffer)
if not success:
invalid = True
else:
setattr(validate_obj, field_name, None)
else:
setattr(validate_obj, field_name, the_value)
if invalid:
row_buffer[0] = logging.ERROR
feedback_row.append(row_buffer)
continue
invariant_errors = []
try:
ITumour.validateInvariants(validate_obj, invariant_errors)
except zope.interface.exceptions.Invalid:
pass
except AttributeError:
pass
errors = [(None, e) for e in invariant_errors]
invalid = False
for error in errors:
if error[0] is None:
msg = error[1].args[0]
msg = translate(_(msg), context=self.request)
row_buffer[2] += msg
invalid = True
if invalid:
row_buffer[0] = logging.ERROR
feedback_row.append(row_buffer)
continue
if not simulation_mode:
obj = validate_obj
old_steps = obj.steps
obj.steps = import_step
notify(StepsChangedEvent(obj, old_steps, import_step))
modified(obj)
msg = translate(_(
u'Import successful: '
u'${sample_title} ${sample_value}; ',
mapping={
'sample_title': sample_title,
'sample_value': sample_value
}),
context=self.request)
if row_buffer[0] < logging.INFO:
row_buffer[0] = logging.INFO
row_buffer[2] += msg
feedback_row.append(row_buffer)
else:
msg = _(u'Invalid import steps.')
api.portal.show_message(msg, self.request, type='error')
logger.error(msg)
success_count += 1
duration = str(timedelta(seconds=(datetime.now() - starttime).seconds))
msg = 'Finished importing {0} tumour objects in {1}'.format(
sheet.nrows - 2, duration)
logger.info(msg)
failed_count = sheet.nrows - 2 - success_count
if success_count:
msg = _(u'${count} item(s) import successfully.',
mapping={'count': success_count})
api.portal.show_message(msg, self.request)
logger.info('{count} item(s) import successfully.'.format(
count=success_count))
if failed_count:
msg = _(u'${count} item(s) import failed.',
mapping={'count': failed_count})
api.portal.show_message(msg, self.request, 'error')
logger.warn(
'{count} item(s) import failed.'.format(count=failed_count))
self.request['feedback_title'] = feedback_title
self.request['feedback_value'] = feedback_row
self.request['feedback_count'] = success_count + failed_count
self.request['success_count'] = success_count
self.request['failed_count'] = failed_count
self.request['duration'] = duration
if all_true_mode and failed_count:
msg = _(u'An error occurred, and the operation aborted.')
api.portal.show_message(msg, self.request, 'error')
logger.info(msg)
transaction.abort()
return self.index()
def testInterface(self):
verifyObject(ITranslationDomain, self._domain)
errors = getValidationErrors(ITranslationDomain, self._domain)
self.assertFalse(errors)
def testInterface(self):
verifyObject(ITranslationDomain, self._domain)
errors = getValidationErrors(ITranslationDomain, self._domain)
self.assertFalse(errors)
def render(self):
if getValidationErrors(IQuotation, self.context):
return u'<abbr title="Schema validation error" class="error schema-validation-error">S</abbr>'
else:
return u''
def __call__(self, data, validate_all=False):
modified = False
errors = []
for schema in iterSchemata(self.context):
write_permissions = mergedTaggedValueDict(
schema, WRITE_PERMISSIONS_KEY)
for name, field in getFields(schema).items():
if field.readonly:
continue
if name in data:
if not self.check_permission(write_permissions.get(name)):
continue
# Deserialize to field value
deserializer = queryMultiAdapter(
(field, self.context, self.request),
IFieldDeserializer)
if deserializer is None:
continue
try:
value = deserializer(data[name])
except ValueError as e:
errors.append({
'message': e.message, 'field': name, 'error': e})
except ValidationError as e:
errors.append({
'message': e.doc(), 'field': name, 'error': e})
else:
f = schema.get(name)
try:
f.validate(value)
except ValidationError as e:
errors.append({
'message': e.doc(), 'field': name, 'error': e})
else:
setattr(schema(self.context), name, value)
if validate_all:
validation = getValidationErrors(schema, schema(self.context))
if len(validation):
for e in validation:
errors.append({
'message': e[1].doc(),
'field': e[0],
'error': e
})
if errors:
raise DeserializationError(errors)
if modified:
notify(ObjectModifiedEvent(self.context))
return self.context
def test_interfaces__IField__3(field):
"""It does not raise `Invalid` if there are values for a choice field."""
field.type = u'Choice'
field.values = [u'sure', u'not really']
errors = getValidationErrors(IField, field)
assert [] == errors
def testInterface(self):
verifyObject(IMessageCatalog, self._catalog)
errors = getValidationErrors(IMessageCatalog, self._catalog)
self.assertFalse(errors)
def testImplementsATGoogleVideo(self):
iface = IATGoogleVideo
self.assertTrue(iface.providedBy(self.video1))
self.assertFalse(getValidationErrors(iface, self.video1))
def testImplementsATContentType(self):
iface = IATContentType
self.assertTrue(iface.providedBy(self.video1))
self.assertFalse(getValidationErrors(iface, self.video1))
def testImplementsImageContent(self):
iface = IImageContent
self.assertTrue(iface.providedBy(self.video1))
self.assertFalse(getValidationErrors(iface, self.video1))
def testInterface(self):
verifyObject(IMessageCatalog, self._catalog)
errors = getValidationErrors(IMessageCatalog, self._catalog)
self.assertFalse(errors)
def test_interfaces__IField__1(field):
"""It does not raise `Invalid` if the field type is not 'choice'."""
field.type = u'Text'
errors = getValidationErrors(IField, field)
assert [] == errors
def _matches(self, item):
errors = getValidationErrors(self.iface, item)
return not errors
