def get_a_sequence_from_dataset():
request_id = request.args.get('requestID', type=int)
from_data_set = request.args.get('fromDataset', 1, type=int)
q_seq = request.args.get('qSeq', type=int)
q_start = request.args.get('qStart', -1, type=int)
q_end = request.args.get('qEnd', -1, type=int)
with lock:
ds_index = current_ds_index if from_data_set else current_q_index
ds_length = onex.getDatasetSeqCount(ds_index)
if (q_seq < 0 or q_seq >= ds_length):
raise InvalidUsage('Sequence index is out of bound')
seq_length = onex.getDatasetSeqLength(ds_index)
if (q_start < 0) or (q_end < 0):
q_start = 0
q_end = seq_length - 1
app.logger.debug('Get sequence %d (%d, %d), fromDataSet = %s', q_seq,
q_start, q_end, from_data_set)
query = _to_string(onex.getSubsequence(ds_index, q_seq, q_start,
q_end))
return jsonify(query=query, requestID=request_id)
def api_dataset_init():
global current_collection_index, current_ds_index
request_id = request.args.get('requestID', type=int)
ds_collection_index = request.args.get('dsCollectionIndex', type=int)
st = request.args.get('st', 0.2, type=float)
with lock:
if ds_collection_index >= len(datasets) or ds_collection_index < 0:
raise InvalidUsage('Dataset collection index out of bound')
if st < 0:
raise InvalidUsage('Invalid similarity threshold value')
# Unload the current dataset in memory
if current_ds_index != -1:
onex.unloadDataset(current_ds_index)
app.logger.debug('Unloaded dataset %d', current_collection_index)
# Load the new dataset
current_collection_index = ds_collection_index
ds_path = str(datasets[current_collection_index].get('path'))
ds_name = str(datasets[current_collection_index].get('name'))
ds_metadata = datasets[current_collection_index].get('metadata')
current_ds_index = onex.loadDataset(ds_path)
metadata = None
if ds_metadata:
with open(ds_metadata) as metadata_file:
metadata = json.load(metadata_file)
else:
app.logger.info('No metadata found for dataset %s', ds_name)
app.logger.debug('Loaded dataset %d [%s]', current_collection_index,
ds_name)
# Normalize the new dataset
app.logger.debug('Normalizing dataset %d', current_collection_index)
normalization = onex.normalizeDataset(current_ds_index)
normalization = {'max': normalization[0], 'min': normalization[1]}
app.logger.info('Normalized dataset %d', current_collection_index)
# Group the new dataset
app.logger.debug('Grouping dataset %d with st = %f',
current_collection_index, st)
num_groups = onex.groupDataset(current_ds_index, st)
app.logger.info('Grouped dataset %d with st = %f. Created %d groups',
current_collection_index, st, num_groups)
# Return number of sequences in the dataset
ds_length = onex.getDatasetSeqCount(current_ds_index)
return jsonify(dsLength=ds_length,
metadata=metadata,
normalization=normalization,
numGroups=num_groups,
requestID=request_id)
def api_find_best_match():
request_id = request.args.get('requestID', type=int)
ds_collection_index = request.args.get('dsCollectionIndex', type=int)
q_find_with_custom_query = request.args.get('qFindWithCustomQuery',
0,
type=int)
q_seq = request.args.get('qSeq', type=int)
q_start = request.args.get('qStart', type=int)
q_end = request.args.get('qEnd', type=int)
if q_start > q_end or q_start < 0 or q_end < 0:
raise InvalidUsage('Invalid starting and ending position')
with lock:
if not (ds_collection_index == current_collection_index):
raise InvalidUsage(
'Dataset {} is not loaded yet'.format(ds_collection_index))
# Index of the dataset containing the query, by default set to the same dataset
# where the best match will be searched from
q_ds_index = current_ds_index
if q_find_with_custom_query:
if current_q_index == -1:
raise InvalidUsage('No custom query is loaded')
# If find with custom query, set to the dataset containing the custom query
q_ds_index = current_q_index
# Get number of sequences in the database containing the query
q_ds_length = onex.getDatasetSeqCount(q_ds_index)
if q_seq < 0 or q_seq >= q_ds_length:
raise InvalidUsage('Sequence index is out of bound')
seq_length = onex.getDatasetSeqLength(q_ds_index)
if q_start >= seq_length or q_end >= seq_length:
raise InvalidUsage('Invalid starting and ending position')
if q_find_with_custom_query:
app.logger.debug(
'Look for best match with sequence %d (%d:%d) in the custom query',
q_seq, q_start, q_end)
else:
app.logger.debug(
'Look for best match with sequence %d (%d:%d) in dataset %d',
q_seq, q_start, q_end, current_collection_index)
r_dist, r_seq, r_start, r_end = \
onex.findSimilar(current_ds_index, q_ds_index, q_seq, q_start, q_end, 0, -1)
group_index = onex.getGroupIndex(current_ds_index, r_seq, r_start,
r_end)
app.logger.debug('Result group index: (%d, %d)', group_index[0],
group_index[1])
result = _to_string(
onex.getSubsequence(current_ds_index, r_seq, r_start, r_end))
warpingPath = onex.getWarpingPath(q_ds_index, q_seq, q_start, q_end,
current_ds_index, r_seq, r_start,
r_end)
return jsonify(result=result,
groupIndex=group_index,
warpingPath=warpingPath,
dist=r_dist,
dsName=datasets[current_collection_index],
seq=r_seq,
start=r_start,
end=r_end,
requestID=request_id)