def validate_and_convert_nexson(nexson, output_version, allow_invalid):
'''Runs the nexson validator and returns a converted 4 object:
nexson, annotation, validation_log, nexson_adaptor
`nexson` is the nexson dict.
`output_version` is the version of nexson syntax to be used after validation.
if `allow_invalid` is False, and the nexson validation has errors, then
a GitWorkflowError will be generated before conversion.
'''
try:
if TRACE_FILES:
_write_to_next_free('input', nexson)
annotation, validation_log, nexson_adaptor = ot_validate(nexson)
if TRACE_FILES:
_write_to_next_free('annotation', annotation)
except:
msg = 'exception in ot_validate: ' + traceback.format_exc()
raise GitWorkflowError(msg)
if (not allow_invalid) and validation_log.has_error():
raise GitWorkflowError('ot_validation failed: ' +
json.dumps(annotation))
nexson = convert_nexson_format(nexson, output_version)
if TRACE_FILES:
_write_to_next_free('converted', nexson)
return nexson, annotation, validation_log, nexson_adaptor
def add_validation_annotation(self, study_obj, sha):
need_to_cache = False
adaptor = None
if self._cache_region is not None:
key = 'v' + sha
annot_event = self._cache_region.get(key, ignore_expiration=True)
if annot_event != NO_VALUE:
_LOG.debug('cache hit for ' + key)
adaptor = NexsonAnnotationAdder()
self._cache_hits += 1
else:
_LOG.debug('cache miss for ' + key)
need_to_cache = True
if adaptor is None:
bundle = ot_validate(study_obj)
annotation = bundle[0]
annot_event = annotation['annotationEvent']
#del annot_event['@dateCreated'] #TEMP
#del annot_event['@id'] #TEMP
adaptor = bundle[2]
replace_same_agent_annotation(study_obj, annot_event)
if need_to_cache:
self._cache_region.set(key, annot_event)
_LOG.debug('set cache for ' + key)
return annot_event
def add_validation_annotation(self, doc_obj, sha):
need_to_cache = False
adaptor = None
annot_event = None
if self._cache_region is not None:
key = 'v' + sha
annot_event = self._cache_region.get(key, ignore_expiration=True)
if annot_event != NO_VALUE:
_LOG.debug('cache hit for ' + key)
adaptor = NexsonAnnotationAdder()
self._cache_hits += 1
else:
_LOG.debug('cache miss for ' + key)
need_to_cache = True
if adaptor is None:
bundle = ot_validate(doc_obj)
annotation = bundle[0]
annot_event = annotation['annotationEvent']
# del annot_event['@dateCreated'] #TEMP
# del annot_event['@id'] #TEMP
adaptor = bundle[2]
replace_same_agent_annotation(doc_obj, annot_event)
if need_to_cache:
self._cache_region.set(key, annot_event)
_LOG.debug('set cache for ' + key)
return annot_event
def testValidFilesPass(self):
format_list = ['1.0', '1.2']
TESTS_WITH_GT_ONE_TREE = ['9']
for d in TESTS_WITH_GT_ONE_TREE:
for nf in format_list:
frag = os.path.join(d, 'v{f}.json'.format(f=nf))
nexson = pathmap.nexson_obj(frag)
annotation = ot_validate(nexson)[0]
self.assertTrue(annotation['annotationEvent']['@passedChecks'])
annotation = ot_validate(nexson, max_num_trees_per_study=1)[0]
self.assertFalse(annotation['annotationEvent']['@passedChecks'])
annotation = ot_validate(nexson, max_num_trees_per_study=1)[0]
self.assertFalse(annotation['annotationEvent']['@passedChecks'])
bundle = validate_and_convert_nexson(nexson,
nf,
allow_invalid=True,
max_num_trees_per_study=1)
nexson, annotation, validation_log, nexson_adaptor = bundle
self.assertFalse(annotation['annotationEvent']['@passedChecks'])
def testValidFilesPass(self):
format_list = ['1.0', '1.2']
TESTS_WITH_GT_ONE_TREE = ['9']
for d in TESTS_WITH_GT_ONE_TREE:
for nf in format_list:
frag = os.path.join(d, 'v{f}.json'.format(f=nf))
nexson = pathmap.nexson_obj(frag)
annotation = ot_validate(nexson)[0]
self.assertTrue(annotation['annotationEvent']['@passedChecks'])
annotation = ot_validate(nexson, max_num_trees_per_study=1)[0]
self.assertFalse(annotation['annotationEvent']['@passedChecks'])
annotation = ot_validate(nexson, max_num_trees_per_study=1)[0]
self.assertFalse(annotation['annotationEvent']['@passedChecks'])
bundle = validate_and_convert_nexson(nexson,
nf,
allow_invalid=True,
max_num_trees_per_study=1)
annotation = bundle[1]
self.assertFalse(annotation['annotationEvent']['@passedChecks'])
def validate_and_convert_nexson(nexson, output_version, allow_invalid, **kwargs):
'''Runs the nexson validator and returns a converted 4 object:
nexson, annotation, validation_log, nexson_adaptor
`nexson` is the nexson dict.
`output_version` is the version of nexson syntax to be used after validation.
if `allow_invalid` is False, and the nexson validation has errors, then
a GitWorkflowError will be generated before conversion.
'''
try:
if TRACE_FILES:
_write_to_next_free('input', nexson)
annotation, validation_log, nexson_adaptor = ot_validate(nexson, **kwargs)
if TRACE_FILES:
_write_to_next_free('annotation', annotation)
except:
msg = 'exception in ot_validate: ' + traceback.format_exc()
raise GitWorkflowError(msg)
if (not allow_invalid) and validation_log.has_error():
raise GitWorkflowError('ot_validation failed: ' + json.dumps(annotation))
nexson = convert_nexson_format(nexson, output_version)
if TRACE_FILES:
_write_to_next_free('converted', nexson)
return nexson, annotation, validation_log, nexson_adaptor
