def __extract_and_validate_nexson(request, repo_nexml2json, kwargs):
try:
nexson = __extract_nexson_from_http_call(request, **kwargs)
bundle = validate_and_convert_nexson(nexson,
repo_nexml2json,
allow_invalid=False)
nexson, annotation, validation_log, nexson_adaptor = bundle
except GitWorkflowError, err:
_LOG = api_utils.get_logger(request, 'ot_api.default.v1')
_LOG.exception('PUT failed in validation')
_raise_HTTP_from_msg(err.msg or 'No message found')
def ingest_new_study(self,
new_study_nexson,
repo_nexml2json,
auth_info,
new_study_id=None):
placeholder_added = False
if new_study_id is not None:
if new_study_id.startswith(self._new_study_prefix):
m = 'Study IDs with the "{}" prefix can only be automatically generated.'.format(
self._new_study_prefix)
raise ValueError(m)
if not STUDY_ID_PATTERN.match(new_study_id):
raise ValueError(
'Study ID does not match the expected pattern of alphabeticprefix_numericsuffix'
)
with self._index_lock:
if new_study_id in self._study2shard_map:
raise ValueError('Study ID is already in use!')
self._study2shard_map[new_study_id] = None
placeholder_added = True
try:
gd, new_study_id = self.create_git_action_for_new_study(
new_study_id=new_study_id)
try:
nexml = new_study_nexson['nexml']
nexml['^ot:studyId'] = new_study_id
bundle = validate_and_convert_nexson(new_study_nexson,
repo_nexml2json,
allow_invalid=True)
nexson, annotation, nexson_adaptor = bundle[0], bundle[
1], bundle[3]
r = self.annotate_and_write(git_data=gd,
nexson=nexson,
study_id=new_study_id,
auth_info=auth_info,
adaptor=nexson_adaptor,
annotation=annotation,
parent_sha=None,
master_file_blob_included=None)
except:
self._growing_shard.delete_study_from_index(new_study_id)
raise
except:
if placeholder_added:
with self._index_lock:
if new_study_id in self._study2shard_map:
del self._study2shard_map[new_study_id]
raise
with self._index_lock:
self._study2shard_map[new_study_id] = self._growing_shard
return new_study_id, r
def ingest_new_study(self,
new_study_nexson,
repo_nexml2json,
auth_info,
new_study_id=None):
placeholder_added = False
if new_study_id is not None:
if new_study_id.startswith(self._new_study_prefix):
m = 'Document IDs with the "{}" prefix can only be automatically generated.'
m = m.format(self._new_study_prefix)
raise ValueError(m)
if not STUDY_ID_PATTERN.match(new_study_id):
raise ValueError('Document ID does not match the expected pattern of alphabeticprefix_numericsuffix')
with self._index_lock:
if new_study_id in self._doc2shard_map:
raise ValueError('Document ID is already in use!')
self._doc2shard_map[new_study_id] = None
placeholder_added = True
try:
gd, new_study_id = self.create_git_action_for_new_study(new_study_id=new_study_id)
try:
nexml = new_study_nexson['nexml']
nexml['^ot:studyId'] = new_study_id
bundle = validate_and_convert_nexson(new_study_nexson,
repo_nexml2json,
allow_invalid=True)
nexson, annotation, nexson_adaptor = bundle[0], bundle[1], bundle[3]
r = self.annotate_and_write(git_data=gd,
nexson=nexson,
doc_id=new_study_id,
auth_info=auth_info,
adaptor=nexson_adaptor,
annotation=annotation,
parent_sha=None,
master_file_blob_included=None)
except:
self._growing_shard.delete_doc_from_index(new_study_id)
raise
except:
if placeholder_added:
with self._index_lock:
if new_study_id in self._doc2shard_map:
del self._doc2shard_map[new_study_id]
raise
with self._index_lock:
self._doc2shard_map[new_study_id] = self._growing_shard
return new_study_id, r
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'])
