def make_request(connection, email_address, galaxy_ids, features, layers, pixel_types):
"""
Makes a request in the database for the provided galaxies.
:param connection: The database connection
:param email_address: The email address requesting the galaxies
:param galaxy_ids: The database IDs of the galaxies
:param features: The features of the galaxies to request
:param layers: The layers of the galaxies to request
:param pixel_types: The pixel types of the galaxies to request
:return:
"""
# Make some new DB entries for these galaxies
transaction = connection.begin()
try:
LOG.info("Making HDF5_REQUEST entry...")
result = connection.execute(HDF5_REQUEST.insert(), profile_id=0, email=email_address,
created_at=datetime.datetime.utcnow())
LOG.info("Making features, layers, pixel types entries...")
insert_features_layers_pixel_types_db_ids(connection, result.inserted_primary_key, features, layers, pixel_types)
LOG.info("Making galaxy entries...")
for galaxy in galaxy_ids:
# We already checked to ensure these are valid, so throw em in.
connection.execute(HDF5_REQUEST_GALAXY.insert(), hdf5_request_id=result.inserted_primary_key,
galaxy_id=galaxy)
transaction.commit()
except:
transaction.rollback()
raise
def make_request(connection, email_address, galaxy_ids, features, layers,
pixel_types):
"""
Makes a request in the database for the provided galaxies.
:param connection: The database connection
:param email_address: The email address requesting the galaxies
:param galaxy_ids: The database IDs of the galaxies
:param features: The features of the galaxies to request
:param layers: The layers of the galaxies to request
:param pixel_types: The pixel types of the galaxies to request
:return:
"""
# Make some new DB entries for these galaxies
transaction = connection.begin()
try:
LOG.info("Making HDF5_REQUEST entry...")
result = connection.execute(HDF5_REQUEST.insert(),
profile_id=0,
email=email_address,
created_at=datetime.datetime.utcnow())
LOG.info("Making features, layers, pixel types entries...")
insert_features_layers_pixel_types_db_ids(connection,
result.inserted_primary_key,
features, layers,
pixel_types)
LOG.info("Making galaxy entries...")
for galaxy in galaxy_ids:
# We already checked to ensure these are valid, so throw em in.
connection.execute(HDF5_REQUEST_GALAXY.insert(),
hdf5_request_id=result.inserted_primary_key,
galaxy_id=galaxy)
transaction.commit()
except:
transaction.rollback()
raise
def generate_files(connection, hdf5_request_galaxy_ids, email, features, layers):
"""
Get the FITS files for this request
:param hdf5_request_galaxy_ids: the galaxy id
:param email:
:param features:
:param layers:
:return:
"""
uuid_string = str(uuid.uuid4())
results = []
for hdf5_request_galaxy in hdf5_request_galaxy_ids:
result = HDF5ToFitsResult()
results.append(result)
connection.execute(HDF5_REQUEST_GALAXY.update().where(HDF5_REQUEST_GALAXY.c.hdf5_request_galaxy_id == hdf5_request_galaxy.hdf5_request_galaxy_id).values(state=1))
try:
galaxy = connection.execute(select([GALAXY]).where(GALAXY.c.galaxy_id == hdf5_request_galaxy.galaxy_id)).first()
result.galaxy_name = galaxy[GALAXY.c.name]
LOG.info('Processing {0} ({1}) for {2}'.format(galaxy[GALAXY.c.name], galaxy[GALAXY.c.galaxy_id], email))
# make sure the galaxy is available
if galaxy[GALAXY.c.status_id] == STORED or galaxy[GALAXY.c.status_id] == DELETED:
output_dir = tempfile.mkdtemp()
try:
s3_helper = S3Helper()
LOG.info('Getting HDF5 file to {0}'.format(output_dir))
tmp_file = get_hdf5_file(s3_helper, output_dir, galaxy[GALAXY.c.name], galaxy[GALAXY.c.run_id], galaxy[GALAXY.c.galaxy_id])
LOG.info('File stored in {0}'.format(tmp_file))
# We have the file
if os.path.isfile(tmp_file):
h5_file = h5py.File(tmp_file, 'r')
galaxy_group = h5_file['galaxy']
pixel_group = galaxy_group['pixel']
file_names = []
for feature in features:
for layer in layers:
LOG.info('Processing {0} - {1}'.format(feature, layer))
file_names.append(build_fits_image(feature, layer, output_dir, galaxy_group, pixel_group, galaxy[GALAXY.c.name]))
h5_file.close()
url = zip_files(s3_helper, get_galaxy_file_name(galaxy[GALAXY.c.name], galaxy[GALAXY.c.run_id], galaxy[GALAXY.c.galaxy_id]), uuid_string, file_names, output_dir)
connection.execute(HDF5_REQUEST_GALAXY.update().
where(HDF5_REQUEST_GALAXY.c.hdf5_request_galaxy_id == hdf5_request_galaxy.hdf5_request_galaxy_id).
values(state=2, link=url, link_expires_at=datetime.now() + timedelta(days=10)))
result.error = None
result.link = url
finally:
# Delete the temp files now we're done
shutil.rmtree(output_dir)
else:
connection.execute(HDF5_REQUEST_GALAXY.update().
where(HDF5_REQUEST_GALAXY.c.hdf5_request_galaxy_id == hdf5_request_galaxy.hdf5_request_galaxy_id).
values(state=3))
result.error = 'Cannot process {0} ({1}) as the HDF5 file has not been generated'.format(galaxy[GALAXY.c.name], galaxy[GALAXY.c.galaxy_id])
LOG.info(result.error)
except:
LOG.error('Major error')
result.error = traceback.format_exc()
connection.execute(HDF5_REQUEST_GALAXY.update().
where(HDF5_REQUEST_GALAXY.c.hdf5_request_galaxy_id == hdf5_request_galaxy.hdf5_request_galaxy_id).
values(state=3))
send_email(email, results, features, layers)
def generate_files(connection, hdf5_request_galaxy_ids, email, features,
layers, pixel_types):
"""
Get the FITS files for this request
:type connection: The database connection
:param pixel_types:
:param hdf5_request_galaxy_ids: the galaxy id
:param email:
:param features:
:param layers:
:return:
"""
uuid_string = str(uuid.uuid4())
results = []
available_galaxies = []
s3_helper = S3Helper()
bucket_name = get_saved_files_bucket()
# Check whether all the requested galaxies are available or not.
for hdf5_request_galaxy in hdf5_request_galaxy_ids:
galaxy = connection.execute(
select([GALAXY]).where(
GALAXY.c.galaxy_id == hdf5_request_galaxy.galaxy_id)).first()
hdf5_request_galaxy = connection.execute(
select([
HDF5_REQUEST_GALAXY
]).where(HDF5_REQUEST_GALAXY.c.hdf5_request_galaxy_id ==
hdf5_request_galaxy.hdf5_request_galaxy_id)).first()
state = hdf5_request_galaxy.state
if state is not 0:
LOG.info('Skipping {0}, state is {1}'.format(
galaxy[GALAXY.c.name], state))
continue # Skip
key = get_key_hdf5(galaxy[GALAXY.c.name], galaxy[GALAXY.c.run_id],
galaxy[GALAXY.c.galaxy_id])
if s3_helper.file_exists(bucket_name, key):
if s3_helper.file_archived(bucket_name, key):
# file is archived
if s3_helper.file_restoring(bucket_name, key):
# if file is restoring, just need to wait for it
LOG.info(
'Galaxy {0} is still restoring from glacier'.format(
galaxy[GALAXY.c.name]))
else:
# if file is not restoring, need to request.
file_size = s3_helper.file_size(bucket_name, key)
if restore_file_size_check(connection, bucket_name,
file_size):
# We're good to restore
LOG.info(
'Making request for archived galaxy {0}'.format(
galaxy[GALAXY.c.name]))
s3_helper.restore_archived_file(bucket_name, key)
connection.execute(
HDF5_REQUEST_GALAXY_SIZE.insert(),
hdf5_request_galaxy_id=hdf5_request_galaxy[
'hdf5_request_galaxy_id'],
size=file_size,
request_time=seconds_since_epoch(datetime.now()))
else:
# Don't restore or we risk spending a lot of money
LOG.info(
'Daily galaxy restore size hit. Cannot request archived galaxy.'
)
else:
# file is not archived
LOG.info('Galaxy {0} is available in s3'.format(
galaxy[GALAXY.c.name]))
available_galaxies.append(hdf5_request_galaxy)
else:
LOG.error('Galaxy {0} does not exist on s3 or glacier!'.format(
galaxy[GALAXY.c.name]))
total_request_galaxies = len(hdf5_request_galaxy_ids)
LOG.info(
'Need to have {0} galaxies available ({1} currently available)'.format(
total_request_galaxies * GALAXY_EMAIL_THRESHOLD,
len(available_galaxies)))
if len(
available_galaxies
) >= total_request_galaxies * GALAXY_EMAIL_THRESHOLD: # Only proceed if more than the threshold of galaxies are available
LOG.info('{0}/{1} (> {2}%) galaxies are available. Email will be sent'.
format(len(available_galaxies), total_request_galaxies,
GALAXY_EMAIL_THRESHOLD * 100))
remaining_galaxies = total_request_galaxies - len(available_galaxies)
for hdf5_request_galaxy in available_galaxies:
result = HDF5ToFitsResult()
results.append(result)
connection.execute(HDF5_REQUEST_GALAXY.update().where(
HDF5_REQUEST_GALAXY.c.hdf5_request_galaxy_id ==
hdf5_request_galaxy.hdf5_request_galaxy_id).values(state=1))
# noinspection PyBroadException
try:
galaxy = connection.execute(
select([GALAXY
]).where(GALAXY.c.galaxy_id ==
hdf5_request_galaxy.galaxy_id)).first()
result.galaxy_name = galaxy[GALAXY.c.name]
LOG.info('Processing {0} ({1}) for {2}'.format(
galaxy[GALAXY.c.name], galaxy[GALAXY.c.galaxy_id], email))
# make sure the galaxy is available
if galaxy[GALAXY.c.status_id] == STORED or galaxy[
GALAXY.c.status_id] == DELETED:
output_dir = tempfile.mkdtemp()
try:
s3_helper = S3Helper()
LOG.info('Getting HDF5 file to {0}'.format(output_dir))
tmp_file = get_hdf5_file(s3_helper, output_dir,
galaxy[GALAXY.c.name],
galaxy[GALAXY.c.run_id],
galaxy[GALAXY.c.galaxy_id])
LOG.info('File stored in {0}'.format(tmp_file))
# We have the file
if os.path.isfile(tmp_file):
int_flux_output = os.path.join(
output_dir, 'intflux')
rad_output = os.path.join(output_dir, 'rad')
if not os.path.exists(int_flux_output):
os.mkdir(int_flux_output)
if not os.path.exists(rad_output):
os.mkdir(rad_output)
file_names = process_hdf5_file(
tmp_file,
galaxy[GALAXY.c.name],
galaxy[GALAXY.c.galaxy_id],
pixel_types,
features,
result,
layers,
output_dir,
rad_output,
int_flux_output,
)
url = zip_files(
s3_helper,
get_galaxy_file_name(
galaxy[GALAXY.c.name],
galaxy[GALAXY.c.run_id],
galaxy[GALAXY.c.galaxy_id]), uuid_string,
file_names, output_dir)
connection.execute(HDF5_REQUEST_GALAXY.update(
).where(
HDF5_REQUEST_GALAXY.c.hdf5_request_galaxy_id ==
hdf5_request_galaxy.hdf5_request_galaxy_id
).values(state=2,
link=url,
link_expires_at=datetime.now() +
timedelta(days=10)))
result.error = None
result.link = url
except S3ResponseError as e: # Handling for a strange s3 error
LOG.error(
'Error retrieving galaxy {0} from s3. Retrying next run'
.format(galaxy[GALAXY.c.name]))
LOG.error('{0}'.format(str(e)))
key = get_key_hdf5(galaxy[GALAXY.c.name],
galaxy[GALAXY.c.run_id],
galaxy[GALAXY.c.galaxy_id])
LOG.info('Key: {0}'.format(key))
LOG.info('Exists: {0}'.format(
s3_helper.file_exists(bucket_name, key)))
result.error = traceback.format_exc()
remaining_galaxies += 1
finally:
# Delete the temp files now we're done
shutil.rmtree(output_dir)
else:
connection.execute(HDF5_REQUEST_GALAXY.update().where(
HDF5_REQUEST_GALAXY.c.hdf5_request_galaxy_id ==
hdf5_request_galaxy.hdf5_request_galaxy_id).values(
state=3))
result.error = 'Cannot process {0} ({1}) as the HDF5 file has not been generated'.format(
galaxy[GALAXY.c.name], galaxy[GALAXY.c.galaxy_id])
LOG.info(result.error)
except:
LOG.error('Major error')
result.error = traceback.format_exc()
connection.execute(HDF5_REQUEST_GALAXY.update().where(
HDF5_REQUEST_GALAXY.c.hdf5_request_galaxy_id ==
hdf5_request_galaxy.hdf5_request_galaxy_id).values(
state=3))
send_email(email, results, features, layers, pixel_types,
remaining_galaxies)
def generate_files(connection, hdf5_request_galaxy_ids, email, features, layers, pixel_types):
"""
Get the FITS files for this request
:type connection: The database connection
:param pixel_types:
:param hdf5_request_galaxy_ids: the galaxy id
:param email:
:param features:
:param layers:
:return:
"""
uuid_string = str(uuid.uuid4())
results = []
available_galaxies = []
s3_helper = S3Helper()
bucket_name = get_saved_files_bucket()
# Check whether all the requested galaxies are available or not.
for hdf5_request_galaxy in hdf5_request_galaxy_ids:
galaxy = connection.execute(select([GALAXY]).where(GALAXY.c.galaxy_id == hdf5_request_galaxy.galaxy_id)).first()
hdf5_request_galaxy = connection.execute(select([HDF5_REQUEST_GALAXY])
.where(HDF5_REQUEST_GALAXY.c.hdf5_request_galaxy_id == hdf5_request_galaxy.hdf5_request_galaxy_id)).first()
state = hdf5_request_galaxy.state
if state is not 0:
LOG.info('Skipping {0}, state is {1}'.format(galaxy[GALAXY.c.name], state))
continue # Skip
key = get_key_hdf5(galaxy[GALAXY.c.name], galaxy[GALAXY.c.run_id], galaxy[GALAXY.c.galaxy_id])
if s3_helper.file_exists(bucket_name, key):
if s3_helper.file_archived(bucket_name, key):
# file is archived
if s3_helper.file_restoring(bucket_name, key):
# if file is restoring, just need to wait for it
LOG.info('Galaxy {0} is still restoring from glacier'.format(galaxy[GALAXY.c.name]))
else:
# if file is not restoring, need to request.
file_size = s3_helper.file_size(bucket_name, key)
if restore_file_size_check(connection, bucket_name, file_size):
# We're good to restore
LOG.info('Making request for archived galaxy {0}'.format(galaxy[GALAXY.c.name]))
s3_helper.restore_archived_file(bucket_name, key)
connection.execute(HDF5_REQUEST_GALAXY_SIZE.insert(),
hdf5_request_galaxy_id=hdf5_request_galaxy['hdf5_request_galaxy_id'],
size=file_size,
request_time=seconds_since_epoch(datetime.now()))
else:
# Don't restore or we risk spending a lot of money
LOG.info('Daily galaxy restore size hit. Cannot request archived galaxy.')
else:
# file is not archived
LOG.info('Galaxy {0} is available in s3'.format(galaxy[GALAXY.c.name]))
available_galaxies.append(hdf5_request_galaxy)
else:
LOG.error('Galaxy {0} does not exist on s3 or glacier!'.format(galaxy[GALAXY.c.name]))
total_request_galaxies = len(hdf5_request_galaxy_ids)
LOG.info('Need to have {0} galaxies available ({1} currently available)'.format(total_request_galaxies * GALAXY_EMAIL_THRESHOLD, len(available_galaxies)))
if len(available_galaxies) >= total_request_galaxies * GALAXY_EMAIL_THRESHOLD: # Only proceed if more than the threshold of galaxies are available
LOG.info('{0}/{1} (> {2}%) galaxies are available. Email will be sent'.format(
len(available_galaxies),
total_request_galaxies,
GALAXY_EMAIL_THRESHOLD * 100)
)
remaining_galaxies = total_request_galaxies - len(available_galaxies)
for hdf5_request_galaxy in available_galaxies:
result = HDF5ToFitsResult()
results.append(result)
connection.execute(HDF5_REQUEST_GALAXY.update().where(HDF5_REQUEST_GALAXY.c.hdf5_request_galaxy_id == hdf5_request_galaxy.hdf5_request_galaxy_id).values(state=1))
# noinspection PyBroadException
try:
galaxy = connection.execute(select([GALAXY]).where(GALAXY.c.galaxy_id == hdf5_request_galaxy.galaxy_id)).first()
result.galaxy_name = galaxy[GALAXY.c.name]
LOG.info('Processing {0} ({1}) for {2}'.format(galaxy[GALAXY.c.name], galaxy[GALAXY.c.galaxy_id], email))
# make sure the galaxy is available
if galaxy[GALAXY.c.status_id] == STORED or galaxy[GALAXY.c.status_id] == DELETED:
output_dir = tempfile.mkdtemp()
try:
s3_helper = S3Helper()
LOG.info('Getting HDF5 file to {0}'.format(output_dir))
tmp_file = get_hdf5_file(s3_helper, output_dir, galaxy[GALAXY.c.name], galaxy[GALAXY.c.run_id], galaxy[GALAXY.c.galaxy_id])
LOG.info('File stored in {0}'.format(tmp_file))
# We have the file
if os.path.isfile(tmp_file):
int_flux_output = os.path.join(output_dir, 'intflux')
rad_output = os.path.join(output_dir, 'rad')
if not os.path.exists(int_flux_output):
os.mkdir(int_flux_output)
if not os.path.exists(rad_output):
os.mkdir(rad_output)
file_names = process_hdf5_file(
tmp_file,
galaxy[GALAXY.c.name],
galaxy[GALAXY.c.galaxy_id],
pixel_types,
features,
result,
layers,
output_dir,
rad_output,
int_flux_output,
)
url = zip_files(
s3_helper,
get_galaxy_file_name(galaxy[GALAXY.c.name], galaxy[GALAXY.c.run_id], galaxy[GALAXY.c.galaxy_id]),
uuid_string,
file_names,
output_dir
)
connection.execute(
HDF5_REQUEST_GALAXY.update().
where(HDF5_REQUEST_GALAXY.c.hdf5_request_galaxy_id == hdf5_request_galaxy.hdf5_request_galaxy_id).
values(state=2, link=url, link_expires_at=datetime.now() + timedelta(days=10)))
result.error = None
result.link = url
except S3ResponseError as e: # Handling for a strange s3 error
LOG.error('Error retrieving galaxy {0} from s3. Retrying next run'.format(galaxy[GALAXY.c.name]))
LOG.error('{0}'.format(str(e)))
key = get_key_hdf5(galaxy[GALAXY.c.name], galaxy[GALAXY.c.run_id], galaxy[GALAXY.c.galaxy_id])
LOG.info('Key: {0}'.format(key))
LOG.info('Exists: {0}'.format(s3_helper.file_exists(bucket_name, key)))
result.error = traceback.format_exc()
remaining_galaxies += 1
finally:
# Delete the temp files now we're done
shutil.rmtree(output_dir)
else:
connection.execute(HDF5_REQUEST_GALAXY.update().
where(HDF5_REQUEST_GALAXY.c.hdf5_request_galaxy_id == hdf5_request_galaxy.hdf5_request_galaxy_id).
values(state=3))
result.error = 'Cannot process {0} ({1}) as the HDF5 file has not been generated'.format(galaxy[GALAXY.c.name], galaxy[GALAXY.c.galaxy_id])
LOG.info(result.error)
except:
LOG.error('Major error')
result.error = traceback.format_exc()
connection.execute(HDF5_REQUEST_GALAXY.update().
where(HDF5_REQUEST_GALAXY.c.hdf5_request_galaxy_id == hdf5_request_galaxy.hdf5_request_galaxy_id).
values(state=3))
send_email(email, results, features, layers, pixel_types, remaining_galaxies)
exit(1)
# Create a new request
# Need to make:
# HDF5_request
# HDF5_request_feature
# HDF5_request_galaxy
# HDF5_request_layer
# HDF5_request_pixel
transaction = connection.begin()
result = connection.execute(HDF5_REQUEST.insert(),
profile_id=47016,
email=args['email'],
created_at=time.time())
connection.execute(HDF5_REQUEST_GALAXY.insert(),
hdf5_request_id=result.inserted_primary_key,
galaxy_id=args['galaxy_id'])
for pixel_type in pixel_types:
connection.execute(HDF5_REQUEST_PIXEL_TYPE.insert(),
hdf5_request_id=result.inserted_primary_key,
hdf5_pixel_type_id=pixel_type +
1) # database entries start at 1
for layer in layers:
connection.execute(HDF5_REQUEST_LAYER.insert(),
hdf5_request_id=result.inserted_primary_key,
hdf5_layer_id=LAYERS[layer] + 1)
for feature in features:
connection = engine.connect()
features, layers, pixel_types = get_features_and_layers_pixeltypes_cmd_line(args)
if len(features) == 0 or len(layers) == 0:
parser.print_help()
exit(1)
# Create a new request
# Need to make:
# HDF5_request
# HDF5_request_feature
# HDF5_request_galaxy
# HDF5_request_layer
# HDF5_request_pixel
transaction = connection.begin()
result = connection.execute(HDF5_REQUEST.insert(), profile_id=47016, email=args['email'], created_at=time.time())
connection.execute(HDF5_REQUEST_GALAXY.insert(), hdf5_request_id=result.inserted_primary_key, galaxy_id=args['galaxy_id'])
for pixel_type in pixel_types:
connection.execute(HDF5_REQUEST_PIXEL_TYPE.insert(), hdf5_request_id=result.inserted_primary_key, hdf5_pixel_type_id=pixel_type+1) # database entries start at 1
for layer in layers:
connection.execute(HDF5_REQUEST_LAYER.insert(), hdf5_request_id=result.inserted_primary_key, hdf5_layer_id=LAYERS[layer]+1)
for feature in features:
connection.execute(HDF5_REQUEST_FEATURE.insert(), hdf5_request_id=result.inserted_primary_key, hdf5_feature_id=FEATURES[feature]+1)
transaction.commit()
LOG.info('All done')
connection.close()
