def _init_data_uri(self):
"""
Create output data URI for the source context (local).
Args:
self: class instance.
Returns:
On success: True.
On failure: False.
"""
# make sure the source data URI has a compatible scheme (local)
if self._parsed_data_uris[self._source_context]['scheme'] != 'local':
msg = 'invalid data uri scheme for this step: {}'.format(
self._parsed_data_uris[self._source_context]['scheme']
)
Log.an().error(msg)
return self._fatal(msg)
# delete old folder if it exists and clean==True
if (
DataManager.exists(
parsed_uri=self._parsed_data_uris[self._source_context]
)
and self._clean
):
if not DataManager.delete(
parsed_uri=self._parsed_data_uris[self._source_context]
):
Log.a().warning(
'cannot delete existing data uri: %s',
self._parsed_data_uris[self._source_context]['chopped_uri']
)
# create folder
if not DataManager.mkdir(
parsed_uri=self._parsed_data_uris[self._source_context],
recursive=True
):
msg = 'cannot create data uri: {}'.format(
self._parsed_data_uris[self._source_context]['chopped_uri']
)
Log.an().error(msg)
return self._fatal(msg)
# create _log folder
if not DataManager.mkdir(
uri='{}/_log'.format(
self._parsed_data_uris[self._source_context]['chopped_uri']
),
recursive=True
):
msg = 'cannot create _log folder in data uri: {}/_log'.format(
self._parsed_data_uris[self._source_context]['chopped_uri']
)
Log.an().error(msg)
return self._fatal(msg)
return True
def _run_map(self, map_item):
"""
Run a job for each map item and store the job ID.
Args:
self: class instance.
map_item: map item object (item of self._map).
Returns:
On success: True.
On failure: False.
"""
# load default app inputs overwrite with template inputs
inputs = {}
for input_key in self._app['inputs']:
if input_key in map_item['template']:
if map_item['template'][input_key]:
# only include an input if the value is a non-empty string
inputs[input_key] = urllib.parse.quote(
str(map_item['template'][input_key]),
safe='/:'
)
else:
if self._app['inputs'][input_key]['default']:
# only include an input if the value is a non-empty string
inputs[input_key] = urllib.parse.quote(
str(self._app['inputs'][input_key]['default']),
safe='/:'
)
# load default app parameters, overwrite with template parameters
parameters = {}
for param_key in self._app['parameters']:
if param_key in map_item['template']:
if self._app['parameters'][param_key]['type'] in ['int', 'long']:
parameters[param_key] = int(map_item['template'][param_key])
elif self._app['parameters'][param_key]['type'] == ['float', 'double']:
parameters[param_key] = float(map_item['template'][param_key])
else:
parameters[param_key] = str(map_item['template'][param_key])
else:
if self._app['parameters'][param_key]['default'] not in [None, '']:
parameters[param_key] \
= self._app['parameters'][param_key]['default']
# add execution method as parameter
parameters['exec_method'] = self._step['execution']['method']
# add execution init commands if 'init' param given
if 'init' in self._step['execution']['parameters']:
parameters['exec_init'] = self._step['execution']['parameters']['init']
# construct agave app template
name = 'gf-{}-{}-{}'.format(
str(map_item['attempt']),
slugify(self._step['name'], regex_pattern=r'[^-a-z0-9_]+'),
slugify(map_item['template']['output'], regex_pattern=r'[^-a-z0-9_]+')
)
name = name[:62]+'..' if len(name) > 64 else name
archive_path = '{}/{}'.format(
self._agave['parsed_archive_uri']['chopped_path'],
name
)
app_template = {
'name': name,
'appId': self._app['implementation']['agave']['agave_app_id'],
'archive': True,
'inputs': inputs,
'parameters': parameters,
'archiveSystem': self._agave['parsed_archive_uri']['authority'],
'archivePath': archive_path
}
# specify processors if 'slots' param given
if 'slots' in self._step['execution']['parameters']:
app_template['processorsPerNode'] = int(
self._step['execution']['parameters']['slots']
)
# specify memory if 'mem' param given
if 'mem' in self._step['execution']['parameters']:
app_template['memoryPerNode'] = '{}'.format(
self._step['execution']['parameters']['mem']
)
Log.some().debug(
"[step.%s]: agave app template:\n%s",
self._step['name'],
pprint.pformat(app_template)
)
# delete archive path if it exists
if DataManager.exists(
uri=self._agave['parsed_archive_uri']['chopped_uri']+'/'+name,
agave=self._agave
):
if not DataManager.delete(
uri=self._agave['parsed_archive_uri']['chopped_uri']+'/'+name,
agave=self._agave
):
Log.a().warning(
'cannot delete archive uri: %s/%s',
self._agave['parsed_archive_uri']['chopped_uri'],
name
)
# submit job
job = self._agave['agave_wrapper'].jobs_submit(app_template)
if not job:
msg = 'agave jobs submit failed for "{}"'.format(
app_template['name']
)
Log.an().error(msg)
return self._fatal(msg)
# log agave job id
Log.some().debug(
'[step.%s]: agave job id: %s -> %s',
self._step['name'],
map_item['template']['output'],
job['id']
)
# record job info
map_item['run'][map_item['attempt']]['agave_job_id'] = job['id']
map_item['run'][map_item['attempt']]['archive_uri'] = '{}/{}'\
.format(
self._agave['parsed_archive_uri']['chopped_uri'],
name
)
map_item['run'][map_item['attempt']]['hpc_job_id'] = ''
# set status of process
map_item['status'] = 'PENDING'
map_item['run'][map_item['attempt']]['status'] = 'PENDING'
return True
def _run_map(self, map_item):
"""
Run a job for each map item and store the job ID.
Args:
self: class instance.
map_item: map item object (item of self._map)
Returns:
On success: True.
On failure: False.
"""
# load default app inputs overwrite with template inputs
inputs = {}
for input_key in self._app['inputs']:
if input_key in map_item['template']:
inputs[input_key] = urllib.parse.quote(str(
map_item['template'][input_key] or ''),
safe='/:')
else:
inputs[input_key] = urllib.parse.quote(str(
self._app['inputs'][input_key]['default'] or ''),
safe='/:')
# load default app parameters, overwrite with template parameters
parameters = {}
for param_key in self._app['parameters']:
if param_key in map_item['template']:
parameters[param_key] = map_item['template'][param_key]
else:
parameters[param_key] \
= self._app['parameters'][param_key]['default']
# add execution method as parameter
parameters['exec_method'] = self._step['execution']['method']
# construct agave app template
name = 'gf-{}-{}-{}'.format(str(map_item['attempt']),
slugify(self._step['name']),
slugify(map_item['template']['output']))
name = name[:62] + '..' if len(name) > 64 else name
archive_path = '{}/{}'.format(
self._agave['parsed_archive_uri']['chopped_path'], name)
app_template = {
'name': name,
'appId': self._app['definition']['agave']['agave_app_id'],
'archive': True,
'inputs': inputs,
'parameters': parameters,
'archiveSystem': self._agave['parsed_archive_uri']['authority'],
'archivePath': archive_path
}
Log.some().debug("agave app template:\n%s",
pprint.pformat(app_template))
# delete archive path if it exists
if DataManager.exists(
uri=self._agave['parsed_archive_uri']['chopped_uri'] + '/' +
name,
agave=self._agave):
if not DataManager.delete(
uri=self._agave['parsed_archive_uri']['chopped_uri'] +
'/' + name,
agave=self._agave):
Log.a().warning(
'cannot delete archive uri: %s/%s',
self._agave['parsed_archive_uri']['chopped_uri'], name)
# submit job
job = self._agave['agave_wrapper'].jobs_submit(app_template)
if not job:
msg = 'agave jobs submit failed for "{}"'.format(
app_template['name'])
Log.an().error(msg)
return self._fatal(msg)
# log agave job id
Log.some().debug('agave job id: %s -> %s',
map_item['template']['output'], job['id'])
# record job info
map_item['run'][map_item['attempt']]['agave_job_id'] = job['id']
map_item['run'][map_item['attempt']]['archive_uri'] = '{}/{}'\
.format(
self._agave['parsed_archive_uri']['chopped_uri'],
name
)
map_item['run'][map_item['attempt']]['hpc_job_id'] = ''
# set status of process
map_item['status'] = 'PENDING'
map_item['run'][map_item['attempt']]['status'] = 'PENDING'
return True
def register_agave_app(self, agave, agave_config, agave_params, agave_publish):
"""
Register app in Agave.
Args:
self: class instance
Returns:
On success: True.
On failure: False.
"""
Log.some().info('registering agave app %s', str(self._path))
Log.some().info('app version: %s', self._config['version'])
# compile agave app template
if not TemplateCompiler.compile_template(
self._path,
'agave-app-def.json.j2',
self._path / 'agave-app-def.json',
version=self._config['version'],
agave=agave_params['agave']
):
Log.a().warning(
'cannot compile agave app "%s" definition from template',
self._app['name']
)
return False
# create main apps URI
parsed_agave_apps_uri = URIParser.parse(
'agave://{}/{}'.format(
agave_params['agave']['deploymentSystem'],
agave_params['agave']['appsDir']
)
)
Log.some().info(
'creating main apps uri: %s',
parsed_agave_apps_uri['chopped_uri']
)
if not DataManager.mkdir(
parsed_uri=parsed_agave_apps_uri,
recursive=True,
agave={
'agave': agave,
'agave_config': agave_config
}
):
Log.a().warning('cannot create main agave apps uri')
return False
# delete app uri if it exists
parsed_app_uri = URIParser.parse(
'agave://{}/{}/{}'.format(
agave_params['agave']['deploymentSystem'],
agave_params['agave']['appsDir'],
self._app['folder']
)
)
Log.some().info(
'deleting app uri if it exists: %s',
parsed_app_uri['chopped_uri']
)
if not DataManager.delete(
parsed_uri=parsed_app_uri,
agave={
'agave': agave,
'agave_config': agave_config
}
):
# log warning, but ignore.. deleting non-existant uri returns False
Log.a().warning(
'cannot delete app uri: %s', parsed_app_uri['chopped_uri']
)
# upload app assets
parsed_assets_uri = URIParser.parse(str(self._path / 'assets'))
Log.some().info(
'copying app assets from %s to %s',
parsed_assets_uri['chopped_uri'],
parsed_app_uri['chopped_uri']
)
if not DataManager.copy(
parsed_src_uri=parsed_assets_uri,
parsed_dest_uri=parsed_app_uri,
local={},
agave={
'agave': agave,
'agave_config': agave_config
}
):
Log.a().warning(
'cannot copy app assets from %s to %s',
parsed_assets_uri['chopped_uri'],
parsed_app_uri['chopped_uri']
)
return False
# upload test script
parsed_test_uri = URIParser.parse(
'{}/{}'.format(
parsed_app_uri['chopped_uri'],
'test'
)
)
Log.some().info(
'creating test uri: %s', parsed_test_uri['chopped_uri']
)
if not DataManager.mkdir(
parsed_uri=parsed_test_uri,
recursive=True,
agave={
'agave': agave,
'agave_config': agave_config
}
):
Log.a().warning(
'cannot create test uri: %s', parsed_test_uri['chopped_uri']
)
return False
parsed_local_test_script = URIParser.parse(
str(self._path / 'test' / 'test.sh')
)
parsed_agave_test_script = URIParser.parse(
'{}/{}'.format(parsed_test_uri['chopped_uri'], 'test.sh')
)
Log.some().info(
'copying test script from %s to %s',
parsed_local_test_script['chopped_uri'],
parsed_agave_test_script['chopped_uri']
)
if not DataManager.copy(
parsed_src_uri=parsed_local_test_script,
parsed_dest_uri=parsed_agave_test_script,
local={},
agave={
'agave': agave,
'agave_config': agave_config
}
):
Log.a().warning(
'cannot copy test script from %s to %s',
parsed_local_test_script['chopped_uri'],
parsed_agave_test_script['chopped_uri']
)
return False
# update existing app, or register new app
Log.some().info('registering agave app')
app_definition = self._yaml_to_dict(
str(self._path / 'agave-app-def.json')
)
if not app_definition:
Log.a().warning(
'cannot load agave app definition: %s',
str(self._path / 'agave-app-def.json')
)
return False
agwrap = AgaveAppsAddUpdate(
agave, agave_config
)
app_add_result = agwrap.call(app_definition)
if not app_add_result:
Log.a().warning(
'cannot register agave app:\n%s', pprint.pformat(app_definition)
)
return False
register_result = {}
# publish app
if agave_publish:
Log.some().info('publishing agave app')
agwrap = AgaveAppsPublish(
agave, agave_config
)
app_publish_result = agwrap.call(app_add_result['id'])
if not app_publish_result:
Log.a().warning(
'cannot publish agave app: %s', app_add_result['id']
)
return False
# return published id and revision
register_result = {
'id': app_publish_result['id'],
'version': self._config['version'],
'revision': 'u{}'.format(app_publish_result['revision'])
}
else:
# return un-published id and blank revision
register_result = {
'id': app_add_result['id'],
'version': self._config['version'],
'revision': ''
}
return register_result