def upload_results(dir):
try:
db = database.Database('default', autocommit=False)
if not os.path.exists(dir) or not os.listdir(dir):
errormsg = 'ERROR: Results directory, %s, does not exist or is empty' % dir
raise upload.UploadNonFatalError(errormsg)
fitsfiles = glob.glob(os.path.join(dir, "*.fits"))
data = datafile.autogen_dataobj(fitsfiles)
version_number = JobUploader.get_version_number(dir)
hdr = header.get_header(fitsfiles)
print "\tHeader parsed."
cands, tempdir = candidates.get_candidates(version_number, dir)
print "\tPeriodicity candidates parsed."
sp_cands = sp_candidates.get_spcandidates(version_number, dir)
print "\tSingle pulse candidates parsed."
for c in (cands + sp_cands):
hdr.add_dependent(c)
diags = diagnostics.get_diagnostics(data.obs_name,
data.beam_id, \
data.obstype, \
version_number, \
dir)
print "\tDiagnostics parsed."
header_id = hdr.upload(db)
for d in diags:
d.upload(db)
print "\tEverything uploaded and checked successfully. header_id=%d" % \
header_id
except (upload.UploadNonFatalError):
exceptionmsgs = traceback.format_exception(*sys.exc_info())
errormsg = "Error while checking results!\n"
errormsg += "\tResults Dir: %s\n\n" % dir
errormsg += "".join(exceptionmsgs)
sys.stderr.write("Error while checking results!\n")
sys.stderr.write("Database transaction will not be committed.\n")
sys.stderr.write("\t%s" % exceptionmsgs[-1])
# Rolling back changes.
db.rollback()
except (database.DatabaseConnectionError, CornellFTP.CornellFTPTimeout,\
upload.UploadDeadlockError, database.DatabaseDeadlockError), e:
# Connection error while uploading. We will try again later.
sys.stderr.write(str(e))
sys.stderr.write("\tRolling back DB transaction and will re-try later.\n")
# Rolling back changes.
db.rollback()
def upload_results(job_submit):
"""
Uploads Results for a given submit.
Input:
job_submit: A row from the job_submits table.
Results from this job submission will be
uploaded.
Output:
None
"""
print "Attempting to upload results"
print "\tJob ID: %d, Job submission ID: %d" % \
(job_submit['job_id'], job_submit['id'])
if debug.UPLOAD:
upload.upload_timing_summary = {}
starttime = time.time()
try:
# Connect to the DB
db = database.Database('SPAN512', autocommit=False)
# Prepare for upload
dir = job_submit['output_dir']
if not os.path.exists(dir) or not os.listdir(dir):
errormsg = 'ERROR: Results directory, %s, does not exist or is empty for job_id=%d' %\
(dir, job_submit['job_id'])
raise upload.UploadNonFatalError(errormsg)
fitsfiles = get_fitsfiles(job_submit)
data = datafile.autogen_dataobj(fitsfiles)
version_number = get_version_number(dir)
if debug.UPLOAD:
parsetime = time.time()
# Upload results
hdr = header.get_header(fitsfiles)
print "\tHeader parsed."
rat_inst_id_cache = ratings2.utils.RatingInstanceIDCache(dbname='nancay')
cands, tempdir = candidates.get_candidates(version_number, dir, \
timestamp_mjd=data.timestamp_mjd, \
inst_cache=rat_inst_id_cache)
print "\tPeriodicity candidates parsed."
sp_cands = sp_candidates.get_spcandidates(version_number, dir, \
timestamp_mjd=data.timestamp_mjd)
print "\tSingle pulse candidates parsed."
for c in (cands + sp_cands):
hdr.add_dependent(c)
diags = diagnostics.get_diagnostics(data.obs_name,
data.beam_id, \
data.obstype, \
version_number, \
dir)
print "\tDiagnostics parsed."
if debug.UPLOAD:
upload.upload_timing_summary['Parsing'] = \
upload.upload_timing_summary.setdefault('Parsing', 0) + \
(time.time()-parsetime)
# Perform the upload
header_id = hdr.upload(db)
for d in diags:
d.upload(db)
print "\tDB upload completed and checked successfully. header_id=%d" % \
header_id
except (upload.UploadNonFatalError):
# Parsing error caught. Job attempt has failed!
exceptionmsgs = traceback.format_exception(*sys.exc_info())
errormsg = "Error while checking results!\n"
errormsg += "\tJob ID: %d, Job submit ID: %d\n\n" % \
(job_submit['job_id'], job_submit['id'])
errormsg += "".join(exceptionmsgs)
sys.stderr.write("Error while checking results!\n")
sys.stderr.write("Database transaction will not be committed.\n")
sys.stderr.write("\t%s" % exceptionmsgs[-1])
queries = []
arglists = []
queries.append("UPDATE job_submits " \
"SET status='upload_failed', " \
"details=\"%s\", " \
"updated_at='%s' " \
"WHERE id=%d"%(errormsg.replace("\"","\'"), jobtracker.nowstr(), job_submit['id']))
queries.append("UPDATE jobs " \
"SET status='failed', " \
"details='Error while uploading results', " \
"updated_at='%s' " \
"WHERE id=%d"%(jobtracker.nowstr(), job_submit['job_id']))
jobtracker.query(queries)
# Rolling back changes.
db.rollback()
except (database.DatabaseConnectionError, \
upload.UploadDeadlockError, database.DatabaseDeadlockError), e:
# Connection error while uploading. We will try again later.
sys.stderr.write(str(e))
sys.stderr.write("\tRolling back DB transaction and will re-try later.\n")
# Rolling back changes.
db.rollback()
def upload_results(job_submit):
"""
Uploads Results for a given submit.
Input:
job_submit: A row from the job_submits table.
Results from this job submission will be
uploaded.
Output:
None
"""
print "Attempting to upload results"
print "\tJob ID: %d, Job submission ID: %d" % \
(job_submit['job_id'], job_submit['id'])
if debug.UPLOAD:
upload.upload_timing_summary = {}
starttime = time.time()
try:
# Connect to the DB
db = database.Database('default', autocommit=False)
# Prepare for upload
dir = job_submit['output_dir']
if not os.path.exists(dir) or not os.listdir(dir):
errormsg = 'ERROR: Results directory, %s, does not exist or is empty for job_id=%d' %\
(dir, job_submit['job_id'])
raise upload.UploadNonFatalError(errormsg)
fitsfiles = get_fitsfiles(job_submit)
data = datafile.autogen_dataobj(fitsfiles)
version_number = get_version_number(dir)
if debug.UPLOAD:
parsetime = time.time()
# Upload results
hdr = header.get_header(fitsfiles)
print "\tHeader parsed."
cands = candidates.get_candidates(version_number, dir)
print "\tPeriodicity candidates parsed."
sp_cands = sp_candidates.get_spcandidates(version_number, dir)
print "\tSingle pulse candidates parsed."
for c in (cands + sp_cands):
hdr.add_dependent(c)
diags = diagnostics.get_diagnostics(data.obs_name,
data.beam_id, \
data.obstype, \
version_number, \
dir)
print "\tDiagnostics parsed."
if debug.UPLOAD:
upload.upload_timing_summary['Parsing'] = \
upload.upload_timing_summary.setdefault('Parsing', 0) + \
(time.time()-parsetime)
# Perform the upload
header_id = hdr.upload(db)
for d in diags:
d.upload(db)
print "\tEverything uploaded and checked successfully. header_id=%d" % \
header_id
except (upload.UploadNonFatalError):
# Parsing error caught. Job attempt has failed!
exceptionmsgs = traceback.format_exception(*sys.exc_info())
errormsg = "Error while checking results!\n"
errormsg += "\tJob ID: %d, Job submit ID: %d\n\n" % \
(job_submit['job_id'], job_submit['id'])
errormsg += "".join(exceptionmsgs)
sys.stderr.write("Error while checking results!\n")
sys.stderr.write("Database transaction will not be committed.\n")
sys.stderr.write("\t%s" % exceptionmsgs[-1])
queries = []
arglists = []
queries.append("UPDATE job_submits " \
"SET status='upload_failed', " \
"details=?, " \
"updated_at=? " \
"WHERE id=?")
arglists.append((errormsg, jobtracker.nowstr(), job_submit['id']))
queries.append("UPDATE jobs " \
"SET status='failed', " \
"details='Error while uploading results', " \
"updated_at=? " \
"WHERE id=?")
arglists.append((jobtracker.nowstr(), job_submit['job_id']))
jobtracker.execute(queries, arglists)
# Rolling back changes.
db.rollback()
except (database.DatabaseConnectionError, CornellFTP.CornellFTPTimeout,\
upload.UploadDeadlockError, database.DatabaseDeadlockError), e:
# Connection error while uploading. We will try again later.
sys.stderr.write(str(e))
sys.stderr.write(
"\tRolling back DB transaction and will re-try later.\n")
# Rolling back changes.
db.rollback()
def upload_results(dir):
try:
db = database.Database('default', autocommit=False)
if not os.path.exists(dir) or not os.listdir(dir):
errormsg = 'ERROR: Results directory, %s, does not exist or is empty' % dir
raise upload.UploadNonFatalError(errormsg)
pdm_dir = os.path.join(
dir, "zerodm") if config.upload.upload_zerodm_periodicity else dir
sp_dir = os.path.join(
dir, "zerodm") if config.upload.upload_zerodm_singlepulse else dir
fitsfiles = glob.glob(os.path.join(dir, "*.fits"))
data = datafile.autogen_dataobj(fitsfiles)
version_number = JobUploader.get_version_number(dir)
hdr = header.get_header(fitsfiles)
print "\tHeader parsed."
rat_inst_id_cache = ratings2.utils.RatingInstanceIDCache(
dbname='common3') #!!!!
#rat_inst_id_cache = ratings2.utils.RatingInstanceIDCache(dbname='MichellePalfaCands')
#cands, tempdir = candidates.get_candidates(version_number, dir)
cands, tempdir = candidates.get_candidates(version_number, pdm_dir, \
timestamp_mjd=data.timestamp_mjd, \
inst_cache=rat_inst_id_cache)
print "\tPeriodicity candidates parsed."
#sp_cands = sp_candidates.get_spcandidates(version_number, dir)
sp_cands, tempdir_sp = sp_candidates.get_spcandidates(version_number, sp_dir, \
timestamp_mjd=data.timestamp_mjd, \
inst_cache=rat_inst_id_cache)
print "\tSingle pulse candidates parsed."
for c in (cands + sp_cands):
hdr.add_dependent(c)
diags = diagnostics.get_diagnostics(data.obs_name,
data.beam_id, \
data.obstype, \
version_number, \
pdm_dir, sp_dir)
print "\tDiagnostics parsed."
header_id = hdr.upload(db)
for d in diags:
d.upload(db)
print "\tEverything uploaded and checked successfully. header_id=%d" % \
header_id
except (upload.UploadNonFatalError):
exceptionmsgs = traceback.format_exception(*sys.exc_info())
errormsg = "Error while checking results!\n"
errormsg += "\tResults Dir: %s\n\n" % dir
errormsg += "".join(exceptionmsgs)
sys.stderr.write("Error while checking results!\n")
sys.stderr.write("Database transaction will not be committed.\n")
sys.stderr.write("\t%s" % exceptionmsgs[-1])
# Rolling back changes.
db.rollback()
except (database.DatabaseConnectionError, CornellFTP.CornellFTPTimeout,\
upload.UploadDeadlockError, database.DatabaseDeadlockError), e:
# Connection error while uploading. We will try again later.
sys.stderr.write(str(e))
sys.stderr.write(
"\tRolling back DB transaction and will re-try later.\n")
# Rolling back changes.
db.rollback()
def upload_results(job_submit):
"""
Uploads Results for a given submit.
Input:
job_submit: A row from the job_submits table.
Results from this job submission will be
uploaded.
Output:
None
"""
print "Attempting to upload results"
print "\tJob ID: %d, Job submission ID: %d\n\tOutput Dir: %s" % \
(job_submit['job_id'], job_submit['id'], job_submit['output_dir'])
if debug.UPLOAD:
upload.upload_timing_summary = {}
starttime = time.time()
try:
# Connect to the DB
db = database.Database('default', autocommit=False)
# Prepare for upload
dir = job_submit['output_dir']
# NEW Beluga - Untar the tarball
import tarfile
to_keep = os.listdir(job_submit['output_dir'])
tarball = glob.glob(job_submit['output_dir'] + '/*00.tgz')[0]
tar = tarfile.open(tarball, 'r:gz')
tar.extractall(path=job_submit['output_dir'])
tar.close()
all_files = os.listdir(job_submit['output_dir'])
to_del = set(all_files) - set(to_keep)
if config.upload.upload_zerodm_periodicity or config.upload.upload_zerodm_singlepulse:
to_keep_zerodm = os.listdir(job_submit['output_dir'] + '/zerodm')
tarball = glob.glob(job_submit['output_dir'] +
'/zerodm/*zerodm.tgz')[0]
tar = tarfile.open(tarball, 'r:gz')
tar.extractall(path=job_submit['output_dir'] + '/zerodm')
tar.close()
all_files_zerodm = os.listdir(job_submit['output_dir'] + '/zerodm')
to_del_zerodm = set(all_files_zerodm) - set(to_keep_zerodm)
pdm_dir = os.path.join(
dir, "zerodm") if config.upload.upload_zerodm_periodicity else dir
sp_dir = os.path.join(
dir, "zerodm") if config.upload.upload_zerodm_singlepulse else dir
if not os.path.exists(dir) or not os.listdir(dir):
errormsg = 'ERROR: Results directory, %s, does not exist or is empty for job_id=%d' %\
(dir, job_submit['job_id'])
raise upload.UploadNonFatalError(errormsg)
elif len(os.listdir(dir)) == 1 and os.listdir(dir)[0] == 'zerodm' \
and not os.listdir(os.path.join(dir,os.listdir(dir)[0])):
errormsg = 'ERROR: Results directory, %s, does not exist or is empty for job_id=%d' %\
(dir, job_submit['job_id'])
raise upload.UploadNonFatalError(errormsg)
fitsfiles = get_fitsfiles(job_submit)
try:
data = datafile.autogen_dataobj(fitsfiles)
except ValueError:
raise upload.UploadNonFatalError
version_number = get_version_number(dir)
if debug.UPLOAD:
parsetime = time.time()
# Upload results
hdr = header.get_header(fitsfiles)
print "\tHeader parsed."
rat_inst_id_cache = ratings2.utils.RatingInstanceIDCache(
dbname='common3')
cands, tempdir = candidates.get_candidates(version_number, pdm_dir, \
timestamp_mjd=data.timestamp_mjd, \
inst_cache=rat_inst_id_cache)
print "\tPeriodicity candidates parsed. (%d cands)" % len(cands)
sp_cands, tempdir_sp = sp_candidates.get_spcandidates(version_number, sp_dir, \
timestamp_mjd=data.timestamp_mjd, \
inst_cache=rat_inst_id_cache)
print "\tSingle pulse candidates parsed. (%d cands)" % len(sp_cands)
diags = diagnostics.get_diagnostics(data.obs_name,
data.beam_id, \
data.obstype, \
version_number, \
pdm_dir, sp_dir)
print "\tDiagnostics parsed."
for c in (cands + sp_cands):
hdr.add_dependent(c)
if debug.UPLOAD:
upload.upload_timing_summary['Parsing'] = \
upload.upload_timing_summary.setdefault('Parsing', 0) + \
(time.time()-parsetime)
# Perform the upload
header_id = hdr.upload(db)
print "Header ID: ", header_id
for d in diags:
d.upload(db)
print "\tDB upload completed and checked successfully. header_id=%d" % \
header_id
except (upload.UploadNonFatalError):
# Parsing error caught. Job attempt has failed!
exceptionmsgs = traceback.format_exception(*sys.exc_info())
errormsg = "Error while checking results!\n"
errormsg += "\tJob ID: %d, Job submit ID: %d\n\n" % \
(job_submit['job_id'], job_submit['id'])
errormsg += "".join(exceptionmsgs)
sys.stderr.write("Error while checking results!\n")
sys.stderr.write("Database transaction will not be committed.\n")
sys.stderr.write("\t%s" % exceptionmsgs[-1])
queries = []
arglists = []
queries.append("UPDATE job_submits " \
"SET status='upload_failed', " \
"details=?, " \
"updated_at=? " \
"WHERE id=?")
arglists.append((errormsg, jobtracker.nowstr(), job_submit['id']))
queries.append("UPDATE jobs " \
"SET status='failed', " \
"details='Error while uploading results', " \
"updated_at=? " \
"WHERE id=?")
arglists.append((jobtracker.nowstr(), job_submit['job_id']))
jobtracker.execute(queries, arglists)
# Rolling back changes.
db.rollback()
except (database.DatabaseConnectionError, ratings2.database.DatabaseConnectionError,\
CornellFTP.CornellFTPTimeout, upload.UploadDeadlockError,\
database.DatabaseDeadlockError), e:
# Connection error while uploading. We will try again later.
sys.stderr.write(str(e))
sys.stderr.write(
"\tRolling back DB transaction and will re-try later.\n")
# Rolling back changes.
db.rollback()