def enqueue_blobs(time_series,queue):
"""config needs psql_connect, resolver"""
config = get_config(CONFIG_FILE, time_series)
feed = IfcbFeed(config.psql_connect)
r = parse_stream(config.resolver)
blob_resolver = r['mvco_blob']
pid_resolver = r['pid']
for lid in feed.latest_bins(n=10000):
if blob_resolver.resolve(pid=lid,time_series=time_series) is None:
pid = pid_resolver.resolve(pid=lid,time_series=time_series).bin_pid
print 'No blobs found for %s, enqueuing' % pid
extract_blobs.apply_async(args=[time_series, pid],queue=queue)
def list_new_filesets(time_series,psql_connect,resolver,after_year=2012):
feed = IfcbFeed(psql_connect)
r = parse_stream(resolver)
for s in list_adcs(time_series,resolver,after_year):
if feed.exists(s.pid):
logging.info('%s EXISTS in time series %s' % (s.pid, time_series))
else:
logging.info('%s NEW, not already in time series %s' % (s.pid, time_series))
fs = r['fileset'].resolve(pid=s.pid,product='raw',time_series=time_series,day_dir=s.day_dir)
if fs is None:
logging.warn('%s UNRESOLVABLE cannot find raw files' % s.pid)
else:
yield fs
def enqueue_features(time_series,queue):
"""config needs psql_connect, resolver"""
config = get_config(CONFIG_FILE, time_series)
feed = IfcbFeed(config.psql_connect)
r = parse_stream(config.resolver)
blob_resolver = r['mvco_blob']
feature_resolver = r['features']
pid_resolver = r['pid']
for lid in feed.latest_bins(n=5000):
if blob_resolver.resolve(pid=lid,time_series=time_series) is not None:
pid = pid_resolver.resolve(pid=lid,time_series=time_series).bin_pid
if feature_resolver.resolve(pid=lid,time_series=time_series) is None:
print 'found blobs but no features for %s' % pid
extract_features.apply_async(args=[time_series, pid],queue=queue)
def accede(config_file, time_series):
config = get_config(config_file, time_series)
logging.info('parsed config file %s:%s' % (config_file, time_series))
fx = IfcbFixity(config.psql_connect)
feed = IfcbFeed(config.psql_connect)
try:
year_pattern = config.year_pattern
except:
year_pattern = '....'
with xa(config.psql_connect) as (c, db):
for s in list_new_filesets(time_series,config.psql_connect,config.resolver,year_pattern=year_pattern): # FIXME hardcoded
try:
check_integrity(s.pid, s.hdr_path, s.adc_path, s.roi_path, s.schema_version)
except Exception, e:
logger.warn('%s FAIL integrity checks: %s' % (s.pid, e))
continue
# hot diggity, we've got some good data
# compute fixity
try:
fx.fix(s.pid, s.hdr_path, cursor=db, filetype='hdr')
logger.info('%s FIXITY computed for %s' % (s.pid, s.hdr_path))
fx.fix(s.pid, s.adc_path, cursor=db, filetype='adc')
logger.info('%s FIXITY computed for %s' % (s.pid, s.adc_path))
fx.fix(s.pid, s.roi_path, cursor=db, filetype='roi')
logger.info('%s FIXITY computed for %s' % (s.pid, s.roi_path))
except:
logger.error('%s FAIL fixity cannot be computed!' % s.pid)
c.rollback()
continue
# register bin
try:
ts = text2utcdatetime(s.date, s.date_format)
feed.create(s.pid, ts, cursor=db)
c.commit()
logger.info('%s DONE' % s.pid)
except:
logger.error('%s FAILED' % s.pid)
continue
logging.info('%s PASS integrity check %s' % (pid, hdr_path))
targets = list(integrity.check_adc(LocalFileSource(adc_path), schema_version=schema_version))
logging.info('%s PASS integrity check %s' % (pid, adc_path))
integrity.check_roi(LocalFileSource(roi_path), targets)
logging.info('%s PASS integrity check %s' % (pid, roi_path))
if __name__=='__main__':
try:
time_series=sys.argv[2]
config = get_config(sys.argv[1], time_series)
except:
sys.stderr.write('usage: [python] oii/ifcb/accession.py [config file] [time series name]\n')
sys.exit(-1)
logging.basicConfig(level=logging.INFO)
fx = IfcbFixity(config.psql_connect)
feed = IfcbFeed(config.psql_connect)
with xa(config.psql_connect) as (c, db):
for s in list_new_filesets(time_series,config.psql_connect,config.resolver,after_year=2005): # FIXME hardcoded
try:
check_integrity(s.pid, s.hdr_path, s.adc_path, s.roi_path, s.schema_version)
except Exception, e:
logging.warn('%s FAIL integrity checks: %s' % (s.pid, e))
continue
# hot diggity, we've got some good data
# compute fixity
try:
fx.fix(s.pid, s.hdr_path, cursor=db, filetype='hdr')
logging.info('%s FIXITY computed for %s' % (s.pid, s.hdr_path))
fx.fix(s.pid, s.adc_path, cursor=db, filetype='adc')
logging.info('%s FIXITY computed for %s' % (s.pid, s.adc_path))
fx.fix(s.pid, s.roi_path, cursor=db, filetype='roi')
try:
time_series = sys.argv[1]
except:
time_series = 'mvco'
config = get_config('./db.conf',time_series)
outdir = config.outdir
psql_connect = '%s dbname=%s' % (config.psql_connect, config.dbname)
R = parse_stream(config.resolver)
NAMESPACE='http://demi.whoi.edu/mvco/'
feed = IfcbFeed(psql_connect)
start=strptime('2005-01-01T00:00:00Z',ISO_8601_FORMAT);
end=strptime('2014-01-01T00:00:00Z',ISO_8601_FORMAT);
with xa(psql_connect) as (c, db):
bin_lids = list(feed.between(start,end))
N=8
pids = []
for n in range(N):
pid = os.fork()
if pid == 0:
outfile = os.path.join(outdir,'scores_%d.csv' % n)
with open(outfile,'w') as of:
for bin_lid in bin_lids[n::N]:
from oii.times import text2utcdatetime, ISO_8601_FORMAT
try:
time_series = sys.argv[1]
except:
time_series = 'mvco'
config = get_config('./db.conf',time_series)
psql_connect = '%s dbname=%s' % (config.psql_connect, config.dbname)
R = parse_stream(config.resolver)
NAMESPACE='http://demi.whoi.edu/mvco/'
feed = IfcbFeed(psql_connect)
start=strptime('2005-01-01T00:00:00Z',ISO_8601_FORMAT);
end=strptime('2014-01-01T00:00:00Z',ISO_8601_FORMAT);
s = 'select count(*) from autoclass where bin_lid=%s'
q = 'insert into autoclass (bin_lid, class_label, roinums, scores) values (%s, %s, %s, %s)'
with xa(psql_connect) as (c, db):
n = 0
for bin_lid in feed.between(start,end):
bin_pid = NAMESPACE + bin_lid
db.execute(s,(bin_lid,))
count = db.fetchone()[0]
if count == 0: