def main():
global POST
input_ = sys.argv[1]
DEBUG_MODE_=DEBUG_MODE
if len(sys.argv) > 2:
DEBUG_MODE_=True
(intervalq,rangeq,sampleq,idq) = (None,None,None,None)
#(intervalq,rangeq,sampleq,idq) = ([],[],[],[])
sys.stderr.write("%s\n" % input_)
if input_[0] == '[' or input_[1] == '[' or input_[2] == '[':
(intervalq,rangeq,sampleq,idq) = parse_json_query(input_)
POST=True
#update support simple '&' CGI format
else:
# (intervalq,rangeq,sampleq,idq) = input_.split('|')
(intervalq,idq,rangeq,sampleq) = process_params(input_)
sample_map = snample.load_sample_metadata(snapconf.SAMPLE_MD_FILE)
if DEBUG_MODE_:
sys.stderr.write("loaded %d samples metadata\n" % (len(sample_map)))
#first we build filter-by-snaptron_id list based either (or all) on passed ids directly
#and/or what's dervied from the sample query and/or what sample ids were passed in as well
#NOTE this is the only place where we have OR logic, i.e. the set of snaptron_ids passed in
#and the set of snaptron_ids dervied from the passed in sample_ids are OR'd together in the filtering
snaptron_ids = set()
if len(idq) >= 1:
query_ids(idq,snaptron_ids)
#if we have any sample related queries, do them to get snaptron_id filter set
#NOTE we are NOT currently support sample-id querying
if len(sampleq) >= 1:
snaptron_ids = snample.query_samples(sampleq,sample_map,snaptron_ids)
#end result here is that we have a list of snaptron_ids to filter by
#or if no snaptron_ids were found we're done, in keeping with the strict AND policy (currently)
#TODO: update this when we start supporting OR in the POSTs, this will need to change
if len(snaptron_ids) == 0 and (len(idq) >=1 or len(sampleq) >= 1):
return
#NOW start normal query processing between: 1) interval 2) range or 3) or just snaptron ids
#note: 1) and 3) use tabix, 2) uses lucene
#sample_set = set()
#UPDATE: prefer tabix queries of either interval or snaptron_ids rather than lucene search of range queries due to speed
#if len(snaptron_ids) > 0 and len(intervalq) == 0 and (len(rangeq) == 0 or not first_tdb):
#back to usual processing, interval queries come first possibly with filters from the point range queries and/or ids
found_snaptron_ids = set()
found_sample_ids = set()
if len(intervalq) >= 1:
(found_snaptron_ids,found_sample_ids) = query_regions(intervalq,rangeq,snaptron_ids,filtering=RESULT_COUNT)
elif len(snaptron_ids) >= 1:
rquery = range_query_parser(rangeq,snaptron_ids)
(found_snaptron_ids,found_sample_ids) = search_introns_by_ids(snaptron_ids,rquery,filtering=RESULT_COUNT)
#finally if there's no interval OR id query to use with tabix, use a point range query (first_rquery) with additional filters from the following point range queries and/or ids in lucene
elif len(rangeq) >= 1:
#run_tabix(first_rquery,rquery,first_tdb,filter_set=snaptron_ids,sample_set=sample_set,debug=DEBUG_MODE_)
(found_snaptron_ids,found_sample_ids) = search_ranges_lucene(rangeq,snaptron_ids,stream_back=True,filtering=RESULT_COUNT)
if RESULT_COUNT:
sys.stdout.write("%d\n" % (len(found_snaptron_ids)))
def main():
input_ = sys.argv[1]
DEBUG_MODE_=DEBUG_MODE
global FORCE_SQLITE
global FORCE_TABIX
if len(sys.argv) == 3:
DEBUG_MODE_=True
if len(sys.argv) == 4:
FORCE_SQLITE=True
if len(sys.argv) == 5:
FORCE_TABIX=True
(intervalq,rangeq,idq) = (None,None,None)
sampleq = []
#(intervalq,rangeq,sampleq,idq) = ([],[],[],[])
sys.stderr.write("%s\n" % input_)
sample_map = snample.load_sample_metadata(snapconf.SAMPLE_MD_FILE)
if DEBUG_MODE_:
sys.stderr.write("loaded %d samples metadata\n" % (len(sample_map)))
#make copy of the region_args tuple
ra = default_region_args
if '[' in input_:
(or_intervals,or_ranges,or_samples,or_ids,ra) = process_post_params(input_)
#(intervalq,rangeq,sampleq,idq) = (or_intervals[0],or_ranges[0],or_samples[0],or_ids[0])
for idx in (xrange(0,len(or_intervals))):
run_toplevel_AND_query(or_intervals[idx],or_ranges[idx],or_samples[idx],or_ids[idx],sample_map=sample_map,ra=ra)
ra=ra._replace(print_header=False)
#update support simple '&' CGI format
else:
(intervalq,idq,rangeq,sampleq,ra) = process_params(input_)
run_toplevel_AND_query(intervalq,rangeq,sampleq,idq,sample_map=sample_map,ra=ra)
def main():
input_ = sys.argv[1]
DEBUG_MODE_ = DEBUG_MODE
global FORCE_SQLITE
global FORCE_TABIX
if len(sys.argv) == 3:
DEBUG_MODE_ = True
if len(sys.argv) == 4:
FORCE_SQLITE = True
if len(sys.argv) == 5:
FORCE_TABIX = True
(intervalq, rangeq, idq) = (None, None, None)
sampleq = []
#(intervalq,rangeq,sampleq,idq) = ([],[],[],[])
sys.stderr.write("%s\n" % input_)
sample_map = snample.load_sample_metadata(snapconf.SAMPLE_MD_FILE)
if DEBUG_MODE_:
sys.stderr.write("loaded %d samples metadata\n" % (len(sample_map)))
#make copy of the region_args tuple
ra = default_region_args
if '[' in input_:
(or_intervals, or_ranges, or_samples, or_ids,
ra) = process_post_params(input_)
#(intervalq,rangeq,sampleq,idq) = (or_intervals[0],or_ranges[0],or_samples[0],or_ids[0])
for idx in (xrange(0, len(or_intervals))):
run_toplevel_AND_query(or_intervals[idx],
or_ranges[idx],
or_samples[idx],
or_ids[idx],
sample_map=sample_map,
ra=ra)
ra = ra._replace(print_header=False)
#update support simple '&' CGI format
else:
(intervalq, idq, rangeq, sampleq, ra) = process_params(input_)
run_toplevel_AND_query(intervalq,
rangeq,
sampleq,
idq,
sample_map=sample_map,
ra=ra)
def main():
input_ = sys.argv[1]
DEBUG_MODE_=DEBUG_MODE
global FORCE_SQLITE
global FORCE_TABIX
if len(sys.argv) == 3:
DEBUG_MODE_=True
if len(sys.argv) == 4:
FORCE_SQLITE=True
if len(sys.argv) == 5:
FORCE_TABIX=True
(intervalq,rangeq,idq) = (None,None,None)
sampleq = []
#(intervalq,rangeq,sampleq,idq) = ([],[],[],[])
sys.stderr.write("%s\n" % input_)
sample_map = snample.load_sample_metadata(snapconf.SAMPLE_MD_FILE)
if DEBUG_MODE_:
sys.stderr.write("loaded %d samples metadata\n" % (len(sample_map)))
#make copy of the region_args tuple
ra = default_region_args
#bulk query mode
#somewhat ad hoc, but with the first test
#trying to avoid a pattern search across the whole input string
#which could be large
if input_[:6] == 'group=' or 'group=' in input_:
for query in re.split(snapconfshared.BULK_QUERY_DELIMITER,input_):
(intervalq,idq,rangeq,sampleq,ra) = process_params(query)
run_toplevel_AND_query(intervalq,rangeq,sampleq,idq,sample_map=sample_map,ra=ra)
elif '[' in input_:
(or_intervals,or_ranges,or_samples,or_ids,ra) = process_post_params(input_)
#(intervalq,rangeq,sampleq,idq) = (or_intervals[0],or_ranges[0],or_samples[0],or_ids[0])
for idx in (xrange(0,len(or_intervals))):
run_toplevel_AND_query(or_intervals[idx],or_ranges[idx],or_samples[idx],or_ids[idx],sample_map=sample_map,ra=ra)
ra=ra._replace(print_header=False)
#update support simple '&' CGI format
else:
(intervalq,idq,rangeq,sampleq,ra) = process_params(input_)
run_toplevel_AND_query(intervalq,rangeq,sampleq,idq,sample_map=sample_map,ra=ra)