def get_parfile_from_id(parfile_id, existdb=None, verify_md5=True):
"""Return the path to the raw file that has the given ID number.
Optionally double check the file's MD5 sum, to make sure
nothing strange has happened.
Inputs:
parfile_id: The ID number of the raw file to get
a path for.
existdb: A (optional) existing database connection object.
(Default: Establish a db connection)
verify_md5: If True, double check the file's MD5 sum.
(Default: Perform MD5 check.)
Output:
fn: The full file path.
"""
notify.print_info("Looking-up raw file with ID=%d" % parfile_id, 2)
# Use the existing DB connection, or open a new one if None was provided
db = existdb or database.Database()
db.connect()
select = db.select([db.parfiles.c.filename, db.parfiles.c.filepath, db.parfiles.c.md5sum]).where(
db.parfiles.c.parfile_id == parfile_id
)
result = db.execute(select)
rows = result.fetchall()
result.close()
if not existdb:
# Close the DB connection we opened
db.close()
if len(rows) == 1:
filename = rows[0]["filename"]
filepath = rows[0]["filepath"]
md5sum_from_db = rows[0]["md5sum"]
else:
raise errors.InconsistentDatabaseError(
"Bad number of files (%d) " "with parfile_id=%d" % (len(rows), parfile_id)
)
fullpath = os.path.join(filepath, filename)
# Make sure the file exists
datafile.verify_file_path(fullpath)
if verify_md5:
notify.print_info(
"Confirming MD5 sum of %s matches what is " "stored in DB (%s)" % (fullpath, md5sum_from_db), 2
)
md5sum_file = datafile.get_md5sum(fullpath)
if md5sum_from_db != md5sum_file:
raise errors.FileError(
"md5sum check of %s failed! MD5 from "
"DB (%s) != MD5 from file (%s)" % (fullpath, md5sum_from_db, md5sum_file)
)
return fullpath
def prep_parfile(fn):
"""Prepare parfile for archiving/loading.
Also, perform some checks on the parfile to make sure we
won't run into problems later. Checks performed:
- Existence of file.
- Read/write access for file (so it can be moved).
Input:
fn: The name of the parfile to check.
Outputs:
params: A dictionary of parameters contained in the file.
NOTE: parameters that look like ints or floats are cast
as such.
"""
# Check existence of file
datafile.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 parameters from file
f = open(fn, "r")
params = {}
for line in f.readlines():
# Ignore blank lines
line = line.strip()
if not line:
continue
key, valstr = line.split()[:2]
if int_re.match(valstr):
# Looks like an int. Cast to int.
val = int(valstr)
elif float_re.match(valstr):
# Looks like a float. Change 'D' to 'E' and cast to float.
val = float(valstr.upper().replace("D", "E"))
else:
# Doesn't seem like a number. Leave as string.
val = valstr
params[key.lower()] = val
if "psrj" in params:
params["pulsar_id"] = cache.get_pulsarid(params["psrj"])
params["name"] = params["psrj"]
elif "psrb" in params:
params["pulsar_id"] = cache.get_pulsarid(params["psrb"])
params["name"] = params["psrb"]
else:
params["pulsar_id"] = cache.get_pulsarid(params["psr"])
params["name"] = params["psr"]
# Translate a few parameters
if "binary" in params:
params["binary_model"] = params["binary"]
if "e" in params:
params["ecc"] = params["e"]
# Do some error checking
if "sini" in params and isinstance(params["sini"], str):
# 'SINI' parameter can be 'KIN' in this case omit 'SINI' from
# the database.
params.pop("sini")
# normalise pulsar name
params["name"] = cache.get_prefname(params["name"])
params["user_id"] = cache.get_userid()
return params
