def fill_process_table(version_id, rawfile_id, parfile_id, template_id,
manip, nchan, nsub, existdb=None):
db = existdb or database.Database()
db.connect()
ins = db.process.insert()
values = {'version_id': version_id,
'rawfile_id': rawfile_id,
'parfile_id': parfile_id,
'template_id': template_id,
'manipulator': manip.name,
'manipulator_args': manip.argstr,
'nchan': nchan,
'nsub': nsub,
'toa_fitting_method': config.cfg.toa_fitting_method,
'user_id': cache.get_userid()}
result = db.execute(ins, values)
process_id = result.inserted_primary_key[0]
result.close()
notify.print_info("Added processing run to DB. Processing ID: %d" %
process_id, 1)
# Close DB connection
if not existdb:
db.close()
return process_id
def main(args):
# Check to make sure user provided a comment
if not args.dry_run and args.comments is None:
raise errors.BadInputError("A comment describing the timfile is "
"required!")
if args.from_file is not None:
# Re-create parser, so we can read arguments from file
parser = utils.DefaultArguments()
add_arguments(parser)
if args.from_file == '-':
argfile = sys.stdin
else:
if not os.path.exists(args.from_file):
raise errors.FileError("The list of cmd line args (%s) "
"does not exist." % args.from_file)
argfile = open(args.from_file, 'r')
for line in argfile:
# Strip comments
line = line.partition('#')[0].strip()
if not line:
# Skip empty line
continue
arglist = shlex.split(line.strip())
args = parser.parse_args(arglist, namespace=args)
# Establish a database connection
db = database.Database()
db.connect()
trans = db.begin()
try:
cmdline = " ".join(sys.argv)
toas = get_toas(args, db)
if debug.is_on('TIMFILE'):
# Check for / handle conflicts
conflict_handler = CONFLICT_HANDLERS[args.on_conflict]
toas = conflict_handler(toas)
wt.write_timfile(toas, {'comments': args.comments,
'user_id': cache.get_userid(),
'add_time': "Not in DB!",
'timfile_id': -1})
elif args.dry_run:
print_summary(toas, args.comments)
else:
conflict_handler = CONFLICT_HANDLERS[args.on_conflict]
timfile_id = add_timfile_entry(toas, cmdline, args.comments,
conflict_handler)
notify.print_info("Created new timfile entry - timfile_id=%d (%s)" %
(timfile_id, utils.give_utc_now()), 1)
except:
db.rollback()
db.close()
raise
else:
db.commit()
db.close()
def add_timfile_entry(toas, cmdline, comments, conflict_handler, existdb=None):
"""Insert a timfile entry in the DB, and associate
TOAs with it.
Inputs:
toas: A list of row objects each representing a TOA.
cmdline: the command line used when running the program.
comments: User comments describing the timfile.
conflict_handler: A handler function to use.
existdb: A (optional) existing database connection object.
(Default: Establish a db connection)
Output:
timfile_id: The resulting ID of the timfile entry.
"""
# Check for / handle conflicts
toas = conflict_handler(toas)
if not toas:
raise errors.ToasterError("No TOAs match criteria provided!")
# Connect to DB, if not using an already-established connection
db = existdb or database.Database()
db.connect()
# Insert timfile entry
ins = db.timfiles.insert()
values = {'user_id': cache.get_userid(),
'version_id': version.get_version_id(db),
'comments': comments,
'pulsar_id': toas[0]['pulsar_id'],
'input_args': cmdline}
result = db.execute(ins, values)
timfile_id = result.inserted_primary_key[0]
result.close()
# Associate the TOAs
ins = db.toa_tim.insert()
values = []
for toa in toas:
values.append({'timfile_id': timfile_id,
'toa_id': toa['toa_id']})
db.execute(ins, values)
if not existdb:
db.close()
return timfile_id
def prep_file(fn):
"""Prepare file for archiving/loading.
Also, perform some checks on the file to make sure we
won't run into problems later. Checks peformed:
- Existence of file.
- Read/write access for file (so it can be moved).
- Header contains all necessary values.
- Site/observing system is recognized.
Input:
fn: The name of the file to check.
Outputs:
params: A dictionary of info to be uploaded.
"""
# Check existence of file
verify_file_path(fn)
# Check file permissions allow for writing and reading
if not os.access(fn, os.R_OK):
raise errors.FileError("File (%s) is not readable!" % fn)
# Grab header info
hdritems = ["nbin", "nchan", "npol", "nsub", "type", "telescop",
"name", "dec", "ra", "freq", "bw", "dm", "rm",
# The names of these header params
# vary with psrchive version
# "dmc", "rm_c", "pol_c",
"scale", "state", "length",
"rcvr", "basis", "backend", "mjd"]
params = get_header_vals(fn, hdritems)
params['user_id'] = cache.get_userid()
# Normalise telescope name
tinfo = cache.get_telescope_info(params['telescop'])
params['telescop'] = tinfo['telescope_name']
params.update(tinfo)
# Check if obssystem_id, pulsar_id, user_id can be found
obssys_key = (params['telescop'].lower(), params['rcvr'].lower(),
params['backend'].lower())
obssys_ids = cache.get_obssystemid_cache()
if obssys_key not in obssys_ids:
t, r, b = obssys_key
raise errors.FileError("The observing system combination in the file "
"%s is not registered in the database. "
"(Telescope: %s, Receiver: %s; Backend: %s)." %
(fn, t, r, b))
else:
params['obssystem_id'] = obssys_ids[obssys_key]
obssysinfo = cache.get_obssysinfo(params['obssystem_id'])
params['band_descriptor'] = obssysinfo['band_descriptor']
params['obssys_name'] = obssysinfo['name']
# Check if pulsar_id is found
try:
psr_id = cache.get_pulsarid(params['name'])
except errors.UnrecognizedValueError:
if config.cfg.auto_add_pulsars:
notify.print_info("Automatically inserting pulsar with "
"name '%s'" % params['name'], 1)
# Add pulsar
psr_id = add_pulsar.add_pulsar(params['name'])
# Force an update of the pulsarid and pulsarname caches
cache.get_pulsarid_cache(update=True)
cache.get_pulsarname_cache(update=True)
else:
raise errors.FileError("The pulsar name %s (from file %s) is not "
"recognized." % (params['name'], fn))
# Normalise pulsar name
params['name'] = cache.get_prefname(params['name'])
params['pulsar_id'] = psr_id
return params
