def _build(self, parsed_args):
"""Build container
"""
if self.build:
try:
self._dockerpy_test()
tag = self._repo_tag()
dockerfile = self._dockerfile()
print_stderr('Building {}'.format(tag))
start_time = milliseconds()
# TODO - build_args, labels, nocache, quiet, forcerm
result = self.dockerpy.images.build(path=self.working_dir,
tag=tag,
dockerfile=dockerfile,
pull=self.pull,
rm=True)
print_stderr('Finished ({} msec)'.format(milliseconds() -
start_time))
for log_line in result[1]:
txt = log_line.get('stream', '').strip()
if txt is not None and txt != '':
self.messages.append(
('build', log_line.get('stream', None)))
return True
except Exception as err:
if self.ignore_errors:
self.messages.append(('push', str(err)))
return False
else:
raise
def _push(self, parsed_args):
"""Push built container
"""
if self.push:
try:
self._dockerpy_test()
tag = self._repo_tag()
print_stderr('Pushing {}'.format(tag))
start_time = milliseconds()
# TODO - auth_config
for log_line in self.dockerpy.images.push(tag,
stream=True,
decode=True):
text_line = log_line.get('status', '').strip()
if text_line not in ('Preparing', 'Waiting',
'Layer already exists', 'Pushing',
'Pushed', 'denied'):
self.messages.append(('push', text_line))
print_stderr('Finished ({} msec)'.format(milliseconds() -
start_time))
return True
except Exception as err:
if self.ignore_errors:
self.messages.append(('push', str(err)))
return False
else:
raise
def _backup(self, parsed_args):
"""Backup existing deployed assets
"""
if self.backup:
dep_sys = self.document['deploymentSystem']
dep_path = self.document['deploymentPath']
backup_dep_path = dep_path + '.' + str(seconds())
print_stderr('Backing up agave://{}/{}'.format(dep_sys, dep_path))
start_time = milliseconds()
self.messages.append(
('backup', 'src: agave://{}/{}'.format(dep_sys, dep_path)))
self.messages.append(
('backup', 'dst: agave://{}/{}'.format(dep_sys,
backup_dep_path)))
try:
manage.move(dep_path,
system_id=dep_sys,
destination=backup_dep_path,
agave=self.tapis_client)
print_stderr('Finished ({} msec)'.format(milliseconds() -
start_time))
return True
except Exception as exc:
self.messages.append(('backup', str(exc)))
print_stderr('Failed ({} msec)'.format(milliseconds() -
start_time))
return False
return True
def take_action(self, parsed_args):
parsed_args = self.preprocess_args(parsed_args)
self.requests_client.setup(API_NAME, SERVICE_VERSION)
self.update_payload(parsed_args)
(storage_system, file_path) = self.parse_url(parsed_args.agave_uri)
headers = ['deleted', 'skipped', 'warnings', 'elapsed_msec']
(deleted, skipped, warnings, elapsed) = [[], [], [], 0]
try:
start_time = milliseconds()
delete(file_path, storage_system, agave=self.tapis_client)
deleted.append(file_path)
elapsed = milliseconds() - start_time
if parsed_args.progress:
print_stderr('Deleted {0}'.format(parsed_args.agave_uri))
except Exception as exc:
skipped.append(file_path)
warnings.append(exc)
if parsed_args.formatter in ('json', 'yaml'):
data = [deleted, skipped, [str(w) for w in warnings], elapsed]
else:
data = [len(deleted), len(skipped), len(warnings), elapsed]
return (tuple(headers), tuple(data))
def _upload(self, parsed_args):
"""Upload asset bundle
"""
if self.upload:
dep_sys = self.document['deploymentSystem']
dep_path = self.document['deploymentPath']
dep_path_parent = os.path.dirname(dep_path)
dep_path_temp = os.path.join(dep_path_parent, self._bundle())
print_stderr('Uploading app bundle to agave://{}/{}'.format(
dep_sys, dep_path))
start_time = milliseconds()
try:
# TODO - incorporate working directory
manage.makedirs(dep_path_parent,
system_id=dep_sys,
permissive=True,
agave=self.tapis_client)
manage.delete(dep_path,
system_id=dep_sys,
permissive=True,
agave=self.tapis_client)
uploaded, skipped, errors, ul_bytes, ec_download = upload.upload(
self._bundle(),
system_id=dep_sys,
destination=dep_path_parent,
progress=True,
agave=self.tapis_client)
manage.move(dep_path_temp,
system_id=dep_sys,
destination=dep_path,
agave=self.tapis_client)
# Rename dep_path_parent/bundle to dep_path
print_stderr('Finished ({} msec)'.format(milliseconds() -
start_time))
for u in uploaded:
self.messages.append(('upload', u))
for e in errors:
self.messages.append(('upload', e))
return True
except Exception as exc:
self.messages.append(('upload', str(exc)))
print_stderr('Failed ({} msec)'.format(milliseconds() -
start_time))
return False
return True
def take_action(self, parsed_args):
parsed_args = self.preprocess_args(parsed_args)
self.requests_client.setup(API_NAME, SERVICE_VERSION)
app_id = AppIdentifier.get_identifier(self, parsed_args)
interactive = parsed_args.interactive
app_def = {}
exc_def = {}
app_def = self.tapis_client.apps.get(appId=app_id)
exc_def = self.tapis_client.systems.get(
systemId=app_def.get('executionSystem'))
# Intrepret parsed_args in light of contents of app and exec system definiitions
# 1. allow --queue to over-ride app['defaultQueue']
exc_queue_names = [q['name'] for q in exc_def['queues']]
queue_name = getattr(parsed_args, 'queue_name', None)
if queue_name is None:
queue_name = app_def.get('defaultQueue', None)
# Get queue details for app execution system
#
# 1. Select either named queue -or- default queue
# 2. ValueError if queue named and not found
sys_queue = None
if queue_name is not None:
for q in exc_def['queues']:
if q['name'] == queue_name:
sys_queue = q
break
else:
for q in exc_def['queues']:
if q['default'] is True:
sys_queue = q
queue_name = sys_queue['name']
break
if sys_queue is None:
raise ValueError(
'Job queue "{0}" does not exist on system "{1}"'.format(
queue_name, exc_def['id']))
# TODO - Rewire so that we can check the queue name after prompting
if interactive:
print('Job configuration')
print('-----------------')
if interactive:
queue_name = prompt('Queue ({0})'.format(
'|'.join(exc_queue_names)),
queue_name,
allow_empty=False)
# Continue interpreting parsed_args
#
# Normally, we could just chain the getattr on parsed_args
# and the successive chained get() to the app definition and
# preferred system queue, but Tapis apps will actually return
# an 'null' value for app.PROPERTY, which translates
# to a value of None for job.PROPERTY.
mem_per_node = getattr(parsed_args, 'memory_per_node',
app_def.get('defaultMemoryPerNode', None))
if mem_per_node is None:
mem_per_node = sys_queue['maxMemoryPerNode']
# if interactive:
# queue_name = int(
# prompt('Memory (GB)', mem_per_node, allow_empty=False))
if isinstance(mem_per_node, int):
mem_per_node = str(mem_per_node) + 'GB'
cpu_per_node = getattr(parsed_args, 'cpu_per_node',
app_def.get('defaultProcessorsPerNode', None))
if cpu_per_node is None:
cpu_per_node = sys_queue['maxProcessorsPerNode']
# if interactive:
# cpu_per_node = int(
# prompt('CPU/Node', cpu_per_node, allow_empty=False))
node_count = getattr(parsed_args, 'node_count',
app_def.get('defaultNodeCount', None))
if node_count is None:
# There is no default node count in a system queue definition
node_count = 1
if interactive:
node_count = int(prompt('Nodes', node_count, allow_empty=False))
# TODO - Validate that max_run_time is LTE sys_queue.maxRequestedTime
max_run_time = getattr(parsed_args, 'max_run_time',
app_def.get('defaultMaxRunTime', None))
if max_run_time is None:
# max_run_time = sys_queue['maxRequestedTime']
max_run_time = DEFAULT_JOB_RUNTIME
if interactive:
max_run_time = prompt('Run Time (max {0})'.format(
sys_queue['maxRequestedTime']),
max_run_time,
allow_empty=False)
# validate max_run_time
if not re.search('[0-9][0-9]:[0-9][0-9]:[0-9][0-9]', max_run_time):
raise ValueError(
'{0} is not a valid job duration. Format must be HH:MM:SS'.
format(max_run_time))
# Safen provided job name or synthesize one if not provided
job_name = getattr(parsed_args, 'job_name', None)
if job_name is not None:
job_name = slugify(job_name, separator='_')
else:
job_name = '{0}-job-{1}'.format(app_def['name'], milliseconds())
if interactive:
job_name = prompt('Job Name', job_name, allow_empty=False)
# Build out the job definition
job = JOB_TEMPLATE
# Populate notifications config
notify_job = not (parsed_args.no_notifications)
if interactive:
notify_job = prompt_boolean('Send status notifications',
notify_job)
if notify_job is True:
try:
if parsed_args.notifications_uri is not None:
nuri = parsed_args.notifications_uri
else:
nuri = self.tapis_client.profiles.get()['email']
if interactive:
nuri = prompt('Status notifications URI',
nuri,
allow_empty=False)
notification = {'event': '*', 'persistent': True, 'url': nuri}
job['notifications'].append(notification)
except Exception:
pass
# Populate archiving config
archive_job = not (parsed_args.no_archive)
if interactive:
archive_job = prompt_boolean('Archive job outputs', archive_job)
job['archive'] = archive_job
if archive_job:
aui = getattr(parsed_args, 'archive_uri', None)
if interactive:
aui = prompt('Archive destination (Agave URI or leave empty)',
aui,
allow_empty=True)
if aui == '':
aui = None
if aui is not None:
asys, apath = parse_uri(parsed_args.archive_uri)
job['archiveSystem'] = asys
job['archivePath'] = apath
# Populate name and resource requirements
job['name'] = job_name
job['appId'] = app_id
job['batchQueue'] = queue_name
job['maxRunTime'] = max_run_time
job['nodeCount'] = node_count
job['processorsPerNode'] = cpu_per_node
job['memoryPerNode'] = mem_per_node
# Populate Inputs
if interactive:
print('Inputs')
print('------')
for inp in app_def.get('inputs', {}):
if inp['value']['visible']:
if inp['value']['required'] or parsed_args.all_fields is True:
job['inputs'][inp['id']] = inp['value'].get('default', '')
if interactive:
inp_label = inp['details']['label']
if inp_label is None or inp_label == '':
inp_label = inp['id']
resp = prompt(inp_label,
job['inputs'][inp['id']],
allow_empty=False)
# Validate URI
if re.search('^(agave://|http://|https://|ftp://)',
resp):
job['inputs'][inp['id']] = resp
else:
raise ValueError(
'Input value {0} must be a URI'.format(resp))
# Populate Parameters
#
# The behavior implemented here is different than the original bash
# jobs-template in that we make no attempt to fake values for
# parameters that don't have a default value
if interactive:
print('Parameters')
print('----------')
for prm in app_def.get('parameters', {}):
if prm['value']['visible']:
if prm['value']['required'] or parsed_args.all_fields is True:
job['parameters'][prm['id']] = prm['value'].get(
'default', '')
if job['parameters'][prm['id']] is None:
job['parameters'][prm['id']] = ''
if interactive:
prm_label = prm['details']['label']
if prm_label is None or prm_label == '':
prm_label = prm['id']
# Typecast and validate response
resp = prompt(prm_label,
job['parameters'][prm['id']],
allow_empty=False)
try:
if prm['value']['type'] in ('string',
'enumeration'):
resp = str(resp)
elif prm['value']['type'] in ('number'):
resp = num(resp)
elif prm['value']['type'] in ('bool', 'flag'):
resp = parse_boolean(resp)
except Exception:
raise ValueError(
'Unable to typecast {0} to type {1}'.format(
resp, prm['value']['type']))
job['parameters'][prm['id']] = resp
# Raw output
outfile_dest = parsed_args.output
if interactive:
outfile_dest = prompt('Output destination',
outfile_dest,
allow_empty=True)
if outfile_dest == '':
of = sys.stdout
else:
of = open(outfile_dest, 'w')
json.dump(job, fp=of, indent=2)
sys.exit(0)
def _upload(self, parsed_args):
"""Upload asset bundle
"""
if self.upload:
dep_sys = self.document['deploymentSystem']
dep_path = self.document['deploymentPath']
dep_path_parent = os.path.dirname(dep_path)
# need the bundle basename for the upload/move workflow to work
bundle_basename = os.path.basename(os.path.normpath(
self._bundle()))
# add date to make tmpdir unique from bundle and deploymentPath
dep_path_temp = os.path.join(dep_path_parent, bundle_basename) \
+ datetime.now().strftime("-%Y-%m-%d")
print_stderr(
'Uploading app asset directory "{0}" to agave://{1}/{2}'.
format(self._bundle(), dep_sys, dep_path))
start_time = milliseconds()
try:
# First, check existence of bundle. No point in taking other action
# if it does not exist
if not os.path.exists(self._bundle()):
raise FileNotFoundError(
'Unable to locate asset directory "{}"'.format(
self._bundle()))
try:
# need relative destination here because
# agavepy permissions check will fail on '/'
# for public systems
manage.makedirs(os.path.basename(dep_path_temp),
system_id=dep_sys,
permissive=True,
destination=dep_path_parent,
agave=self.tapis_client)
# clear out destination directory
manage.delete(dep_path,
system_id=dep_sys,
permissive=True,
agave=self.tapis_client)
except Exception as err:
self.messages.append(('upload', str(err)))
# upload bundle to tmp dir
uploaded, skipped, errors, ul_bytes, ec_download = upload.upload(
self._bundle(),
system_id=dep_sys,
destination=dep_path_temp,
progress=True,
agave=self.tapis_client)
# move tmp dir bundle to the destination dir
manage.move(os.path.join(dep_path_temp, bundle_basename),
system_id=dep_sys,
destination=dep_path,
agave=self.tapis_client)
# delete tmp dir
manage.delete(dep_path_temp,
system_id=dep_sys,
permissive=True,
agave=self.tapis_client)
print_stderr('Finished ({} msec)'.format(milliseconds() -
start_time))
for u in uploaded:
self.messages.append(('upload', u))
for e in errors:
self.messages.append(('upload', e))
if len(errors) > 0:
if self.ignore_errors is False:
raise Exception('Upload failures: {}'.format(
errors.join(';')))
return True
except Exception as exc:
if self.ignore_errors:
self.messages.append(('upload', str(exc)))
print_stderr('Failed ({} msec)'.format(milliseconds() -
start_time))
return False
else:
raise
return True