def _run_state():
"""Uses a state file with a timestamp to control which files will be
retrieved from the CSA ftp host.
Ingestion is based on fully-qualified file names from the CSA ftp host,
because those are difficult to reproduce otherwise.
"""
builder = nbc.FileNameBuilder(NEOSSatName)
config = mc.Config()
config.get_executors()
state = mc.State(config.state_fqn)
start_time = state.get_bookmark(NEOS_BOOKMARK)
temp = mc.increment_time(start_time, 0).timestamp()
todo_list, max_timestamp = scrape.build_todo(
temp, config.working_directory, config.state_fqn)
max_date = datetime.fromtimestamp(max_timestamp)
incremental_source = data_source.IncrementalSource(todo_list)
transferrer = tc.FtpTransfer(config.data_source)
return rc.run_by_state(config=config, name_builder=builder,
command_name=APPLICATION,
bookmark_name=NEOS_BOOKMARK,
meta_visitors=META_VISITORS,
data_visitors=DATA_VISITORS,
end_time=max_date, chooser=None,
source=incremental_source,
store_transfer=transferrer)
def _run_by_public():
"""Run the processing for observations that are public, but there are
no artifacts representing the previews in CAOM, or a FITS file in ad.
Called as gem_run_public. The time-boxing is based on timestamps from a
state.yml file. Call once/day, since data release timestamps have times
of 00:00:00.000.
:return 0 if successful, -1 if there's any sort of failure. Return status
is used by airflow for task instance management and reporting.
"""
config = mc.Config()
config.get_executors()
external_metadata.init_global(config=config)
name_builder = nbc.FileNameBuilder(gem_name.GemName)
incremental_source = data_source.PublicIncremental(config)
meta_visitors = _define_meta_visitors(config)
return rc.run_by_state(config=config,
name_builder=name_builder,
command_name=main_app.APPLICATION,
bookmark_name=data_source.GEM_BOOKMARK,
meta_visitors=meta_visitors,
data_visitors=DATA_VISITORS,
end_time=None,
source=incremental_source,
chooser=None)
def _run_state():
"""Uses a state file with a timestamp to control which entries will be
processed.
"""
config = mc.Config()
config.get_executors()
return rc.run_by_state(name_builder=nbc.FileNameBuilder(VliteName),
command_name=APPLICATION,
meta_visitors=META_VISITORS,
data_visitors=DATA_VISITORS)
def _run():
"""
Uses a todo file to identify the work to be done.
:return 0 if successful, -1 if there's any sort of failure. Return status
is used by airflow for task instance management and reporting.
"""
name_builder = nbc.FileNameBuilder(get_storage_name)
return rc.run_by_todo(name_builder=name_builder,
meta_visitors=META_VISITORS,
data_visitors=DATA_VISITORS)
def _run_state():
"""Uses a state file with a timestamp to control which entries will be
processed.
"""
config = mc.Config()
config.get_executors()
source = dsc.QueryTimeBoxDataSource(config, preview_suffix='png')
name_builder = nbc.FileNameBuilder(dao_name.DAOName)
return rc.run_by_state(name_builder=name_builder,
command_name=APPLICATION,
bookmark_name=DAO_BOOKMARK,
meta_visitors=META_VISITORS,
data_visitors=DATA_VISITORS,
source=source)
def _run():
"""
Uses a todo file to identify the work to be done.
:return 0 if successful, -1 if there's any sort of failure. Return status
is used by airflow for task instance management and reporting.
"""
name_builder = nbc.FileNameBuilder(PHANGSName)
return rc.run_by_todo(config=None,
name_builder=name_builder,
command_name=APPLICATION,
meta_visitors=META_VISITORS,
data_visitors=DATA_VISITORS,
chooser=None)
def _run_state():
"""Uses a state file with a timestamp to control which entries will be
processed.
"""
name_builder = nbc.FileNameBuilder(PHANGSName)
return rc.run_by_state(config=None,
name_builder=name_builder,
command_name=APPLICATION,
bookmark_name=None,
meta_visitors=META_VISITORS,
data_visitors=DATA_VISITORS,
end_time=None,
source=None,
chooser=None)
def _run():
"""
Uses a todo file to identify the work to be done.
:return 0 if successful, -1 if there's any sort of failure. Return status
is used by airflow for task instance management and reporting.
"""
builder = nbc.FileNameBuilder(NEOSSatName)
config = mc.Config()
config.get_executors()
transferrer = tc.FtpTransfer(config.data_source)
return rc.run_by_todo(name_builder=builder,
config=config,
command_name=APPLICATION,
meta_visitors=META_VISITORS,
data_visitors=DATA_VISITORS,
store_transfer=transferrer)
def _run_remote():
"""
Uses a todo file to identify the work to be done.
:return 0 if successful, -1 if there's any sort of failure. Return status
is used by airflow for task instance management and reporting.
"""
config = mc.Config()
config.get_executors()
name_builder = nbc.FileNameBuilder(GemProcName)
vos_client = Client(vospace_certfile=config.proxy_fqn)
store_transfer = tc.VoFitsTransfer(vos_client)
data_source = dsc.VaultListDirDataSource(vos_client, config)
return rc.run_by_todo(config=config,
name_builder=name_builder,
command_name=APPLICATION,
source=data_source,
meta_visitors=META_VISITORS,
data_visitors=DATA_VISITORS,
store_transfer=store_transfer)
def _run_by_incremental():
"""Run incremental processing for observations that are posted on the site
archive.gemini.edu. TODO in the future this will depend on the incremental
query endpoint.
:return 0 if successful, -1 if there's any sort of failure. Return status
is used by airflow for task instance management and reporting.
"""
config = mc.Config()
config.get_executors()
state = mc.State(config.state_fqn)
end_timestamp_s = state.bookmarks.get(data_source.GEM_BOOKMARK).get(
'end_timestamp', datetime.now())
end_timestamp_dt = mc.make_time_tz(end_timestamp_s)
logging.info(f'{main_app.APPLICATION} will end at {end_timestamp_s}')
external_metadata.init_global(config=config)
name_builder = nbc.FileNameBuilder(gem_name.GemName)
incremental_source = data_source.IncrementalSource()
meta_visitors = _define_meta_visitors(config)
result = rc.run_by_state(
config=config,
name_builder=name_builder,
command_name=main_app.APPLICATION,
bookmark_name=data_source.GEM_BOOKMARK,
meta_visitors=meta_visitors,
data_visitors=DATA_VISITORS,
end_time=end_timestamp_dt,
source=incremental_source,
chooser=None,
)
if incremental_source.max_records_encountered:
logging.warning('!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!')
logging.warning('Encountered maximum records!!')
logging.warning('!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!')
result |= -1
return result
def test_run_state_v(client_mock, repo_mock):
repo_mock.return_value.read.side_effect = tc.mock_read
client_mock.get_node.side_effect = tc.mock_get_node
# the test file is length 0
client_mock.return_value.copy.return_value = 0
test_wd = '/usr/src/app/caom2pipe/int_test'
caom2pipe_bookmark = 'caom2_timestamp'
test_config = mc.Config()
test_config.working_directory = test_wd
test_config.collection = 'TEST'
test_config.interval = 10
test_config.log_file_directory = f'{test_wd}/logs'
test_config.failure_fqn = \
f'{test_config.log_file_directory}/failure_log.txt'
test_config.log_to_file = True
test_config.logging_level = 'DEBUG'
test_config.progress_file_name = 'progress.txt'
test_config.proxy_file_name = f'{test_wd}/cadcproxy.pem'
test_config.rejected_file_name = 'rejected.yml'
test_config.rejected_directory = f'{test_wd}/rejected'
test_config._report_fqn = f'{test_config.log_file_directory}/app_report.txt'
test_config.resource_id = 'ivo://cadc.nrc.ca/sc2repo'
test_config.retry_file_name = 'retries.txt'
test_config.retry_fqn = \
f'{test_config.log_file_directory}/{test_config.retry_file_name}'
test_config.state_file_name = 'state.yml'
test_config.success_fqn = \
f'{test_config.log_file_directory}/success_log.txt'
test_config.tap_id = 'ivo://cadc.nrc.ca/sc2tap'
test_config.task_types = [
mc.TaskType.STORE, mc.TaskType.INGEST, mc.TaskType.MODIFY
]
test_config.features.use_file_names = True
test_config.features.use_urls = False
test_config.features.supports_latest_client = True
test_config.use_local_files = False
if not os.path.exists(test_wd):
os.mkdir(test_wd)
# if this test is failing, did the docker container get
# restarted recently?
# first create /caom2pipe_test/1000003f.fits.fz,
# then check that the test_start_time and test_end_time values
# correspond somewhat to the timestamp on that file
#
# this timestamp is 15 minutes earlier than the timestamp of the
# file in /caom2pipe_test
#
test_start_time = '2021-05-08 02:25:09'
with open(test_config.state_fqn, 'w') as f:
f.write('bookmarks:\n')
f.write(f' {caom2pipe_bookmark}:\n')
f.write(f' last_record: {test_start_time}\n')
test_end_time = datetime(2021,
5,
8,
2,
41,
27,
965132,
tzinfo=timezone.utc)
with open(test_config.proxy_fqn, 'w') as f:
f.write('test content\n')
test_data_source = TestListDirTimeBoxDataSource()
test_builder = nbc.FileNameBuilder(tc.TestStorageName)
transferrer = TestTransfer()
try:
test_result = rc.run_by_state(
bookmark_name=caom2pipe_bookmark,
command_name='collection2caom2',
config=test_config,
end_time=test_end_time,
name_builder=test_builder,
source=test_data_source,
modify_transfer=None,
store_transfer=transferrer,
)
assert test_result is not None, 'expect a result'
assert test_result == 0, 'expect success'
assert client_mock.return_value.copy.called, 'expect put call'
args, kwargs = client_mock.return_value.copy.call_args
assert args[0] == 'ad:TEST/test_obs_id.fits.gz', 'wrong args[0]'
assert (args[1] == '/usr/src/app/caom2pipe/int_test/test_obs_id/'
'test_obs_id.fits'), 'wrong args[1]'
# state file checking
test_state = mc.State(test_config.state_fqn)
assert test_state is not None, 'expect state content'
test_checkpoint = test_state.get_bookmark(caom2pipe_bookmark)
assert test_checkpoint == test_end_time, 'wrong bookmark'
# success file testing
assert os.path.exists(test_config.log_file_directory), 'log directory'
assert os.path.exists(test_config.success_fqn), 'success fqn'
assert os.path.exists(test_config.progress_fqn), 'progress fqn'
log_file = f'{test_config.log_file_directory}/test_obs_id.log'
actual = glob.glob(f'{test_config.log_file_directory}/**')
assert os.path.exists(log_file), f'specific log file {actual}'
xml_file = f'{test_config.log_file_directory}/test_obs_id.fits.xml'
assert os.path.exists(xml_file), f'xml file {actual}'
# reporting testing
report_file = f'{test_config.log_file_directory}/app_report.txt'
assert os.path.exists(report_file), f'report file {actual}'
pass_through_test = False
with open(report_file, 'r') as f:
for line in f:
pass_through_test = True
if 'Number' in line:
bits = line.split(':')
found = False
if 'Inputs' in bits[0]:
assert bits[1].strip() == '1', 'wrong inputs'
found = True
elif 'Successes' in bits[0]:
assert bits[1].strip() == '1', 'wrong successes'
found = True
elif 'Timeouts' in bits[0]:
assert bits[1].strip() == '0', 'wrong timeouts'
found = True
elif 'Retries' in bits[0]:
assert bits[1].strip() == '0', 'wrong retries'
found = True
elif 'Errors' in bits[0]:
assert bits[1].strip() == '0', 'wrong errors'
found = True
elif 'Rejections' in bits[0]:
assert bits[1].strip() == '0', 'wrong rejections'
found = True
assert found, f'{line}'
assert pass_through_test, 'found a report file and checked it'
finally:
f_list = glob.glob(f'{test_wd}/**', recursive=True)
for entry in f_list:
try:
if os.path.isdir(entry):
os.rmdir(entry)
else:
os.unlink(entry)
except OSError as e:
logging.error(f'failed to delete {e}')
