def check_running_jobs(self):
"""
Check the status/progress of all map-reduce items and update _map status.
Args:
self: class instance.
Returns:
True.
"""
# check if procs are running, finished, or failed
for map_item in self._map:
try:
if ShellWrapper.is_running(
map_item['run'][map_item['attempt']]['proc']
):
map_item['status'] = 'RUNNING'
else:
if map_item['run'][map_item['attempt']]['proc'].returncode:
map_item['status'] = 'FAILED'
else:
map_item['status'] = 'FINISHED'
map_item['run'][map_item['attempt']]['status']\
= map_item['status']
except (OSError, AttributeError) as err:
Log.a().warning(
'process polling failed for map item "%s" [%s]',
map_item['filename'], str(err)
)
map_item['status'] = 'FAILED'
self._update_status_db(self._status, '')
return True
def apply_job_modifiers(jobs_dict, job_mods):
"""Update the jobs_dict with the given modifiers."""
for mod in job_mods:
# split at =
try:
parts = mod.split('=')
except ValueError as err:
Log.a().warning('job mod "%s" is malformed [%s]', mod, str(err))
continue # skip mod
key = parts[0]
if not key:
Log.a().warning('empty job mod')
continue # skip mod
val = None
if len(parts) == 1:
# only one key, treat as bool switch
val = True
elif len(parts) == 2:
# two parts, key & value
val = parts[1]
else:
# multiple '=', include '=' in value
val = '='.join(parts[1:])
# split key at .
keys = key.split('.')
# apply to all jobs
for job in jobs_dict.values():
set_dict_key_list(job, keys, val)
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 _copy_asset(self, asset):
"""
Copy app assets.
Args:
self: class instance
asset: what to copy
Returns:
On success: True.
On failure: False.
"""
if not self._copy_prefix:
Log.a().warning(
'copy prefix must be specified when copying app assets'
)
return False
if not asset.get('dst'):
Log.a().warning('asset dst required for app %s', self._app['name'])
return False
if not asset.get('src'):
Log.a().warning('asset src required for app %s', self._app['name'])
return False
# create asset destination
asset_path = Path(self._path / asset['dst'])
asset_path.mkdir(exist_ok=True)
if 'zip' in asset:
# create a tar.gz of src
cmd = 'tar -czf "{}" --directory="{}" .'.format(
str(Path(asset_path / '{}.tar.gz'.format(asset['zip']))),
str(Path(self._copy_prefix) / asset['src'])
)
Log.some().info('zipping: %s', cmd)
cmd_result = ShellWrapper.invoke(cmd)
if cmd_result is False:
Log.a().warning('cannot zip asset src: %s', cmd)
return False
Log.some().info('tar stdout: %s', cmd_result)
else:
# move without creating tar.gz
cmd = 'cp -R "{}" "{}"'.format(
str(Path(self._copy_prefix) / asset['src']),
str(asset_path)
)
Log.some().info('copying: %s', cmd)
cmd_result = ShellWrapper.invoke(cmd)
if cmd_result is False:
Log.a().warning('cannot copy asset src: %s', cmd)
return False
Log.some().info('copy stdout: %s', cmd_result)
return True
def _send_notifications(self, status):
# construct message
msg_data = {
'to': '',
'from': '*****@*****.**',
'subject': 'GeneFlow Job "{}": {}'.format(
self._job['name'], status
),
'content': (
'Your GeneFlow job status has changed to {}'
'\nJob Name: {}'
'\nJob ID: {}'
).format(status, self._job['name'], self._job_id)
}
# use agave token as header if available
if 'agave' in self._workflow_context:
msg_headers = {
'Authorization':'Bearer {}'.format(
self._workflow_context['agave']\
.get_context_options()['agave_wrapper']\
._agave.token.token_info.get('access_token')
)
}
else:
msg_headers = {}
Log.some().info('message headers: %s', str(msg_headers))
for notify in self._job['notifications']:
Log.some().info(
'sending notification(s) to %s @ %s',
str(notify['to']),
notify['url'],
)
to_list = notify['to']
if isinstance(notify['to'], str):
to_list = [notify['to']]
for to_item in to_list:
msg_data['to'] = to_item
try:
response = requests.post(
notify['url'], data=msg_data, headers=msg_headers
)
except requests.exceptions.RequestException as err:
Log.a().warning(
'cannot send notification to %s @ %s: %s',
to_item, notify['url'], str(err)
)
if response.status_code != 201:
Log.a().warning(
'cannot send notification to %s @ %s: %s',
to_item, notify['url'], response.text
)
def retry_failed(self, map_item):
"""
Retry a job.
Args:
self: class instance.
Returns:
True if failed/stopped job restarted successfully
False if failed/stopped job not restarted due to error
"""
# retry job
Log.some().info(
'[step.%s]: retrying agave job (%s), attempt number %s',
self._step['name'],
map_item['template']['output'],
map_item['attempt']+1
)
# add another run to list
map_item['attempt'] += 1
map_item['run'].append({})
if not self._run_map(map_item):
Log.a().warning(
'[step.%s]: cannot retry agave job (%s), attempt number %s',
self._step['name'],
map_item['template']['output'],
map_item['attempt']
)
return False
return True
def compile_template(template_path, template_name, compiled_name,
**kwargs):
"""
Compile a GeneFlow template file.
Args:
template_path: search path for templates. If omitted, the
GeneFlow package path of data/templates is used.
template_name: name of the template file, must be stored in
data/templates of the GeneFlow source package.
compiled_name: full path of the compiled target file.
kwargs: data to populate the template.
Returns:
On success: True.
On failure: False.
"""
# set default template path
if not template_path:
template_path = GF_PACKAGE_PATH / 'data/templates'
# load template
try:
template_loader = jinja2.FileSystemLoader(
searchpath=str(template_path))
template_env = jinja2.Environment(loader=template_loader,
trim_blocks=True,
lstrip_blocks=True)
template = template_env.get_template(template_name)
except jinja2.TemplateSyntaxError as err:
Log.an().warning('cannot load template, syntax error: %s [%s, %s]',
template_name, str(err), str(err.lineno))
return False
except jinja2.TemplateError as err:
Log.an().warning('cannot load template: %s [%s]', template_name,
str(err))
return False
# compile and write
try:
with open(str(compiled_name), 'w') as compiled_file:
compiled_file.write(template.render(**kwargs))
except IOError as err:
Log.an().warning('cannot write compiled template file: %s [%s]',
compiled_name, str(err))
return False
except jinja2.TemplateError as err:
Log.a().warning('cannot compile template: %s [%s]', template_name,
str(err))
return False
return True
def __del__(self):
"""
Disconnect from drmaa session when workflow class is deleted.
Args:
None.
Returns:
Nothing.
"""
try:
self._drmaa_session.exit()
except drmaa.errors.DrmaaException as err:
Log.a().warning('cannot exit drmaa session: [%s]', str(err))
def _re_init():
"""Reinit drmaa session."""
# exit existing session
try:
self._drmaa_session.exit()
except drmaa.errors.DrmaaException as err:
Log.a().warning('cannot exit drmaa session: [%s]', str(err))
# initialize session again
try:
self._drmaa_session.initialize()
except drmaa.errors.DrmaaException as err:
Log.an().error('cannot initialize drmaa session: [%s]', str(err))
return False
return True
def apply_job_modifiers(jobs_dict, job_mods):
"""Update the jobs_dict with the given modifiers."""
for mod in job_mods:
# split at =
try:
key, val = mod.split('=')
except ValueError as err:
Log.a().warning('job mod "%s" is malformed [%s]', mod, str(err))
continue # skip mod
# split key at .
keys = key.split('.')
# apply to all jobs
for job in jobs_dict.values():
set_dict_key_list(job, keys, val)
def check_running_jobs(self):
"""
Check the status/progress of all map-reduce items and update _map status.
Args:
self: class instance.
Returns:
True.
"""
# check if jobs are running, finished, or failed
for map_item in self._map:
if map_item['status'] != 'FINISHED' and map_item[
'status'] != 'FAILED':
# can only get job status if it has not already been disposed with "wait"
status = self._gridengine['drmaa_session'].jobStatus(
map_item['run'][map_item['attempt']]['hpc_job_id'])
map_item['status'] = self._job_status_map[status]
if map_item['status'] == 'FINISHED' or map_item[
'status'] == 'FAILED':
# check exit status
job_info = self._gridengine['drmaa_session'].wait(
map_item['run'][map_item['attempt']]['hpc_job_id'],
self._gridengine['drmaa_session'].TIMEOUT_NO_WAIT)
Log.a().debug('[step.%s]: exit status: %s -> %s',
self._step['name'],
map_item['template']['output'],
job_info.exitStatus)
if job_info.exitStatus > 0:
# job actually failed
map_item['status'] = 'FAILED'
map_item['run'][map_item['attempt']]['status'] = map_item['status']
if map_item['status'] == 'FAILED' and map_item['attempt'] < 5:
# retry job if not at limit
if not self.retry_failed(map_item):
Log.a().warning(
'[step.%s]: cannot retry failed gridengine job (%s)',
self._step['name'], map_item['template']['output'])
self._update_status_db(self._status, '')
return True
def check_running_jobs(self):
"""
Check the status/progress of all map-reduce items and update _map status.
Args:
self: class instance.
Returns:
True.
"""
# check if procs are running, finished, or failed
for map_item in self._map:
if map_item['status'] in ['RUNNING', 'UNKNOWN']:
try:
if not ShellWrapper.is_running(
map_item['run'][map_item['attempt']]['proc']):
returncode = map_item['run'][
map_item['attempt']]['proc'].returncode
if returncode:
map_item['status'] = 'FAILED'
else:
map_item['status'] = 'FINISHED'
Log.a().debug('[step.%s]: exit status: %s -> %s',
self._step['name'],
map_item['template']['output'],
returncode)
# decrease num running procs
if self._num_running > 0:
self._num_running -= 1
except (OSError, AttributeError) as err:
Log.a().warning(
'process polling failed for map item "%s" [%s]',
map_item['filename'], str(err))
map_item['status'] = 'UNKNOWN'
map_item['run'][map_item['attempt']]['status']\
= map_item['status']
self._update_status_db(self._status, '')
return True
def check_running_jobs(self):
"""
Check the status/progress of all map-reduce items and update _map status.
Args:
self: class instance.
Returns:
True.
"""
# check if jobs are running, finished, or failed
for map_item in self._map:
if map_item['status'] not in ['FINISHED', 'FAILED', 'PENDING']:
try:
# can only get job status if it has not already been disposed with "wait"
status = self._slurm['drmaa_session'].jobStatus(
map_item['run'][map_item['attempt']]['hpc_job_id'])
map_item['status'] = self._job_status_map[status]
except drmaa.DrmCommunicationException as err:
msg = 'cannot get job status for step "{}" [{}]'\
.format(self._step['name'], str(err))
Log.a().warning(msg)
map_item['status'] = 'UNKNOWN'
if map_item['status'] in ['FINISHED', 'FAILED']:
# check exit status
job_info = self._slurm['drmaa_session'].wait(
map_item['run'][map_item['attempt']]['hpc_job_id'],
self._slurm['drmaa_session'].TIMEOUT_NO_WAIT)
Log.a().debug('[step.%s]: exit status: %s -> %s',
self._step['name'],
map_item['template']['output'],
job_info.exitStatus)
if job_info.exitStatus > 0:
# job actually failed
map_item['status'] = 'FAILED'
# decrease num running procs
if self._num_running > 0:
self._num_running -= 1
map_item['run'][map_item['attempt']]['status'] = map_item['status']
if map_item['status'] == 'FAILED' and map_item['attempt'] < 5:
if self._throttle_limit == 0 or self._num_running < self._throttle_limit:
# retry job if not at retry or throttle limit
if not self.retry_failed(map_item):
Log.a().warning(
'[step.%s]: cannot retry failed slurm job (%s)',
self._step['name'], map_item['template']['output'])
else:
self._num_running += 1
self._update_status_db(self._status, '')
return True
def upload_agave_test_data(self):
"""
Upload Agave test data from workflow package.
Args:
self: class instance.
Returns:
None
"""
if (not self._agave or not self._agave_params
or not self._agave_params.get('agave')):
Log.a().warning(
'must provide agave parameters to upload test data')
return False
# create main test data URI
parsed_base_test_uri = URIParser.parse('agave://{}/{}'.format(
self._agave_params['agave']['deploymentSystem'],
self._agave_params['agave']['testDataDir']))
Log.some().info('creating base test data uri: %s',
parsed_base_test_uri['chopped_uri'])
if not DataManager.mkdir(parsed_uri=parsed_base_test_uri,
recursive=True,
agave={
'agave': self._agave,
'agave_config': self._config['agave']
}):
Log.a().warning('cannot create base test data uri: %s',
parsed_base_test_uri['chopped_uri'])
return False
# upload test data
parsed_local_test_uri = URIParser.parse(str(Path(self._path) / 'data'))
parsed_agave_test_uri = URIParser.parse('{}/{}'.format(
parsed_base_test_uri['chopped_uri'],
Path(self._path).name))
Log.some().info('copying test data from %s to %s',
parsed_local_test_uri['chopped_uri'],
parsed_agave_test_uri['chopped_uri'])
if not DataManager.copy(parsed_src_uri=parsed_local_test_uri,
parsed_dest_uri=parsed_agave_test_uri,
local={},
agave={
'agave': self._agave,
'agave_config': self._config['agave']
}):
Log.a().warning('cannot copy test data from %s to %s',
parsed_local_test_uri['chopped_uri'],
parsed_agave_test_uri['chopped_uri'])
return False
return True
def _update_status_db(self, status, msg):
"""
Update workflow status in DB.
Args:
self: class instance
status: Workflow status
msg: Success, error or warning message
Returns:
On success: True.
On failure: False.
"""
try:
data_source = DataSource(self._config['database'])
except DataSourceException as err:
msg = 'data source initialization error [{}]'.format(str(err))
Log.an().error(msg)
return False
# set start time (if started, or errored immediatedly)
if (
status in ['RUNNING', 'ERROR']
and self._status == 'PENDING'
):
if not data_source.set_job_started(self._job_id):
Log.a().warning('cannot set job start time in data source')
data_source.rollback()
# set finished time (even on error)
if status in ['FINISHED', 'ERROR']:
if not data_source.set_job_finished(self._job_id):
Log.a().warning('cannot set job finish time in data source')
data_source.rollback()
# if state change, contact notification endpoint
if status != self._status:
if self._job['notifications']:
self._send_notifications(status)
# update database
self._status = status
if not data_source.update_job_status(self._job_id, status, msg):
Log.a().warning('cannot update job status in data source')
data_source.rollback()
data_source.commit()
return True
def switch_context(cls, uri, new_base_uri):
"""
Change the context of uri to the new_base.
new_base can have a different scheme and base URL. If uri has no 'name'
(e.g., ends with /), then the new context URI is identical to the
normalized new_base_uri.
Args:
uri: URI to change context.
new_base_uri: base URI of the new context.
Returns:
On success: parsed URI in new context.
On failure: False.
"""
# validate URIs
parsed_uri = cls.parse(uri)
if not parsed_uri:
Log.a().debug('invalid uri: %s', uri)
return False
parsed_new_base_uri = cls.parse(new_base_uri)
if not parsed_new_base_uri:
Log.a().debug('invalid new base uri: %s', new_base_uri)
return False
# construct URI in new context
new_uri = '{}:{}{}{}'.format(
parsed_new_base_uri['scheme'],
('//{}'.format(parsed_new_base_uri['authority'])
if parsed_new_base_uri['authority'] else ''),
parsed_new_base_uri['chopped_path'],
('{}' if parsed_new_base_uri['chopped_path'] == '/' else
'/{}').format(parsed_uri['name']))
# parse the new URI to validate
parsed_new_uri = cls.parse(new_uri)
if not parsed_new_uri:
Log.a().debug('invalid new uri: %s', new_uri)
return False
return parsed_new_uri
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 parse(cls, uri):
"""
Parse a URI and return components. If the scheme is missing, it..
defaults to "local".
Args:
uri: A generic URI string.
Returns:
On success: A dict that contains "uri", "scheme", "authority", and
"path", etc:
{
"uri": original URI
"chopped_uri": normalized URI
"scheme":
"authority":
"path": full path
"chopped_path": normalized path
"folder": folder part of path (to last slash, not including
last slash
"name": folder/file name, part of path after last slash
}
On failure: False.
"""
matched = re.match(cls.uri_regex, str(uri))
if not matched:
Log.a().debug('invalid uri: %s', uri)
return False
# extract scheme, e.g., local, agave, http, etc.
scheme = matched.group(2)
if not scheme:
scheme = 'local'
# authority can be '' (e.g., server, or storage system)
authority = matched.group(4) if matched.group(4) else ''
path = matched.group(5) if matched.group(5) else '/'
# replace one or more consecutive slashes with single slash
path = re.sub('/+', '/', path)
# get folder and name from path
matched = re.match(cls.path_regex, path)
if not matched:
Log.a().debug('invalid path of uri: %s', path)
return False
folder = matched.group(1) if matched.group(1) else matched.group(2)
name = matched.group(3) if matched.group(3) else ''
# "normalized" path without extra slashes
chopped_path = (folder +
name if folder == '/' or folder == '' else folder +
'/' + name) if name else folder
# "normalized" URI without extra slashes and with scheme
chopped_uri = '{}{}{}'.format(
'{}:'.format(scheme),
('//{}'.format(authority) if authority else ''), chopped_path)
return {
'uri': uri, # original URI
'chopped_uri': chopped_uri,
'scheme': scheme,
'authority': authority,
'path': path,
'chopped_path': chopped_path,
'folder': folder,
'name': name
}
def install_assets(self):
"""
Install app assets.
Args:
self: class instance
Returns:
On success: True.
On failure: False.
"""
# set asset type
default_asset = self._app_asset
# if not set on CLI, use asset type specified in workflow apps-repo
if not default_asset:
default_asset = self._app.get('asset')
# if not set in workflow apps-repo, use app default
if not default_asset:
default_asset = self._config.get('default_asset')
Log.some().info('installing app asset type: %s', str(default_asset))
if not default_asset:
# no asset type specified, nothing left to do
return True
if 'assets' not in self._config:
# app is not configured with any assets
return True
if default_asset not in self._config['assets']:
# if asset type is not listed in config, display warning and
# continue
Log.a().warning(
'unconfigured asset type specified: %s', str(default_asset)
)
return True
assets = self._config['assets'][default_asset]
# install all components for asset
for asset in assets:
Log.some().info('app asset:\n%s', pprint.pformat(asset))
if 'type' not in asset:
Log.a().warning('asset type missing for app "%s"', self._app['name'])
continue
if asset['type'] == 'copy':
if not self._copy_asset(asset):
Log.a().warning(
'cannot copy assets for app "%s"', self._app['name']
)
continue
elif asset['type'] == 'build':
if not self._build_asset(asset):
Log.a().warning(
'cannot build assets for app "%s"', self._app['name']
)
continue
else:
Log.a().warning(
'invalid asset type "%s" for app "%s"',
asset['type'], self._app['name']
)
return True
def _build_asset(self, asset):
"""
Build app assets.
Args:
self: class instance
asset: what to build
Returns:
On success: True.
On failure: False.
"""
# make sure the build path exists
build_path = self._path / 'build'
build_path.mkdir(exist_ok=True)
build_repo_path = None
if not asset.get('folder'):
Log.a().warning(
'repo folder must be set when specifying a build asset'
)
return False
# clone build repo
build_repo_path = build_path / asset['folder']
if asset.get('repo'):
# if repo is set, clone and build it
try:
if asset.get('tag'):
Repo.clone_from(
asset['repo'], str(build_repo_path),
branch=asset['tag'], config='http.sslVerify=false'
)
else:
Repo.clone_from(
asset['repo'], str(build_repo_path),
config='http.sslVerify=false'
)
except GitError as err:
Log.an().error(
'cannot clone git repo for build: %s [%s]',
asset['repo'], str(err)
)
return False
# if repo is not set, packaged build scripts are included with the
# workflow in the build_repo_path
# build
cmd = 'make -C "{}"'.format(str(build_repo_path))
Log.some().info('build command: %s', cmd)
cmd_result = ShellWrapper.invoke(cmd)
if cmd_result is False:
Log.a().warning('cannot build app: %s', cmd)
return False
Log.some().info('make stdout: %s', cmd_result)
# move built assets
# make sure asset folder exists
if not asset.get('dst'):
Log.a().warning('asset dst required for app %s', self._app['name'])
return False
if not asset.get('src'):
Log.a().warning('asset src required for app %s', self._app['name'])
return False
# create asset destination
asset_path = self._path / asset['dst']
asset_path.mkdir(exist_ok=True)
# set src path
src_path = self._path / asset['src']
if 'zip' in asset:
# create a tar.gz of src
cmd = 'tar -czf "{}" --directory="{}" .'.format(
str(asset_path / '{}.tar.gz'.format(asset['zip'])),
str(src_path)
)
Log.some().info('zipping: %s', cmd)
cmd_result = ShellWrapper.invoke(cmd)
if cmd_result is False:
Log.a().warning('cannot zip asset src: %s', cmd)
return False
Log.some().info('tar stdout: %s', cmd_result)
else:
# move without creating tar.gz
cmd = 'mv "{}" "{}"'.format(str(src_path), str(asset_path))
Log.some().info('moving: %s', cmd)
cmd_result = ShellWrapper.invoke(cmd)
if cmd_result is False:
Log.a().warning('cannot move asset src: %s', cmd)
return False
Log.some().info('mv stdout: %s', cmd_result)
return True
def load(self, yaml_path):
"""
Load and validate GeneFlow definition from a multi-doc YAML file.
Read a GeneFlow definition file, which can contain apps, workflows,
and jobs. Loaded docs are appended to the _apps, _workflows, and _jobs
arrays. Load may be called multiple times. Docs are only added if
successfully validated.
Args:
yaml_path: path to GeneFlow YAML definition file.
Returns:
On success: True
On failure: False.
"""
# load multi-doc yaml file
gf_def = self.load_yaml(yaml_path)
if gf_def is False:
Log.an().error('cannot load yaml file: %s', yaml_path)
return False
# iterate through yaml docs
for gf_doc in gf_def:
# class must be specified, either app or workflow
if 'class' not in gf_doc:
Log.a().error('unspecified document class')
return False
if gf_doc['class'] == 'app':
if 'apps' in gf_doc:
# this is a list of apps
for app in gf_doc['apps']:
if not self.add_app(app):
Log.an().error('invalid app in definition: %s',
yaml_path)
return False
else:
# only one app
if not self.add_app(gf_doc):
Log.an().error('invalid app in definition: %s',
yaml_path)
return False
elif gf_doc['class'] == 'workflow':
# only one workflow per yaml file allowed
if not self.add_workflow(gf_doc):
Log.an().error('invalid workflow in definition: %s',
yaml_path)
return False
elif gf_doc['class'] == 'job':
if 'jobs' in gf_doc:
# this is a list of jobs
for job in gf_doc['jobs']:
if not self.add_job(job):
Log.an().error('invalid job in definition: %s',
yaml_path)
return False
else:
# only one job
if not self.add_job(gf_doc):
Log.an().error('invalid job in definition: %s',
yaml_path)
return False
else:
Log.a().error('invalid document class: %s', gf_doc['class'])
return False
return True
def _run_map(self, map_item):
"""
Run a job for each map item and store the proc and PID.
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] = map_item['template'][input_key]
else:
if self._app['inputs'][input_key]['default']:
inputs[input_key] = self._app['inputs'][input_key]['default']
# 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:
if self._app['parameters'][param_key]['default'] not in [None, '']:
parameters[param_key] \
= self._app['parameters'][param_key]['default']
# construct shell command
cmd = self._app['implementation']['local']['script']
for input_key in inputs:
if inputs[input_key]:
cmd += ' --{}="{}"'.format(
input_key,
URIParser.parse(inputs[input_key])['chopped_path']
)
for param_key in parameters:
if param_key == 'output':
cmd += ' --output="{}/{}"'.format(
self._parsed_data_uris[self._source_context]\
['chopped_path'],
parameters['output']
)
else:
cmd += ' --{}="{}"'.format(
param_key, parameters[param_key]
)
# add exeuction method
cmd += ' --exec_method="{}"'.format(self._step['execution']['method'])
# specify execution init commands if 'init' param given
if 'init' in self._step['execution']['parameters']:
cmd += ' --exec_init="{}"'.format(self._step['execution']['parameters']['init'])
# add stdout and stderr
log_path = '{}/_log/gf-{}-{}-{}'.format(
self._parsed_data_uris[self._source_context]['chopped_path'],
map_item['attempt'],
slugify(self._step['name'], regex_pattern=r'[^-a-z0-9_]+'),
slugify(map_item['template']['output'], regex_pattern=r'[^-a-z0-9_]+')
)
cmd += ' > "{}.out" 2> "{}.err"'.format(log_path, log_path)
Log.a().debug('command: %s', cmd)
# launch process
proc = ShellWrapper.spawn(cmd)
if proc is False:
msg = 'shell process error: {}'.format(cmd)
Log.an().error(msg)
return self._fatal(msg)
# record job info
map_item['run'][map_item['attempt']]['proc'] = proc
map_item['run'][map_item['attempt']]['pid'] = proc.pid
# set status of process
map_item['status'] = 'RUNNING'
map_item['run'][map_item['attempt']]['status'] = 'RUNNING'
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
def install_apps(self):
"""
Install apps for the workflow package.
Args:
self: class instance.
Returns:
None
"""
apps_path = Path(self._path) / 'workflow' / 'apps'
if self._clean:
# remove apps folder
if apps_path.is_dir():
shutil.rmtree(str(apps_path))
# create apps folder if not already there
apps_path.mkdir(exist_ok=True)
for app in self._apps_repo['apps']:
if self._app_name == app['name'] or not self._app_name:
Log.some().info('app:\n%s', pprint.pformat(app))
repo_path = apps_path / app['folder']
# create AppInstaller instance
app_installer = AppInstaller(str(repo_path), app,
self._app_asset,
self._copy_prefix)
# clone app into install location
if not app_installer.clone_git_repo():
Log.an().error('cannot clone app to %s', str(repo_path))
# skip app
continue
if not app_installer.load_config():
Log.an().error('cannot load app config.yaml')
# skip app
continue
if self._make_apps:
if not app_installer.make():
Log.an().error('cannot compile app templates')
# skip app
continue
if not app_installer.install_assets():
Log.an().error('cannot install app assets')
# skip app
continue
# register in Agave
if (self._agave and self._agave_params
and self._agave_params.get('agave')):
register_result = app_installer.register_agave_app(
self._agave, self._config['agave'], self._agave_params,
self._agave_publish)
if not register_result:
Log.a().warning('cannot register app "%s" in agave',
app['name'])
# skip app
continue
Log.some().info('registered agave app:\n%s',
pprint.pformat(register_result))
# compile jinja template for published app definition
if not TemplateCompiler.compile_template(
repo_path,
'app.yaml.j2',
repo_path / 'app.yaml',
agave=self._agave_params['agave'],
version=register_result['version'],
revision=register_result['revision']):
Log.a().warning(
'cannot compile app "%s" definition from template',
app['name'])
# skip app
continue
else:
# compile jinja template for app definition
if not TemplateCompiler.compile_template(
repo_path, 'app.yaml.j2', repo_path / 'app.yaml'):
Log.a().warning(
'cannot compile app "%s" definition from template',
app['name'])
# skip app
continue
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] = map_item['template'][input_key]
else:
if self._app['inputs'][input_key]['default']:
inputs[input_key] = self._app['inputs'][input_key][
'default']
# 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:
if self._app['parameters'][param_key]['default'] not in [
None, ''
]:
parameters[param_key] \
= self._app['parameters'][param_key]['default']
# get full path of wrapper script
path = shutil.which(self._app['implementation']['local']['script'])
if not path:
msg = 'wrapper script not found in path: %s'.format(
self._app['implementation']['local']['script'])
Log.an().error(msg)
return self._fatal(msg)
# construct argument list for wrapper script
args = [path]
for input_key in inputs:
if inputs[input_key]:
args.append('--{}={}'.format(
input_key,
URIParser.parse(inputs[input_key])['chopped_path']))
for param_key in parameters:
if param_key == 'output':
args.append('--output={}/{}'.format(
self._parsed_data_uris[self._source_context][0]\
['chopped_path'],
parameters['output']
))
else:
args.append('--{}={}'.format(param_key, parameters[param_key]))
# add exeuction method
args.append('--exec_method={}'.format(
self._step['execution']['method']))
# specify execution init commands if 'init' param given
if 'init' in self._step['execution']['parameters']:
args.append('--exec_init={}'.format(
self._step['execution']['parameters']['init']))
Log.a().debug('[step.%s]: command: %s -> %s', self._step['name'],
map_item['template']['output'], ' '.join(args))
# construct job name
name = 'gf-{}-{}-{}'.format(
map_item['attempt'],
slugify(self._step['name'], regex_pattern=r'[^-a-z0-9_]+'),
slugify(map_item['template']['output'],
regex_pattern=r'[^-a-z0-9_]+'))
# construct paths for logging stdout and stderr
log_path = '{}/_log/{}'.format(
self._parsed_data_uris[self._source_context][0]['chopped_path'],
name)
# create and populate job template
jt = self._slurm['drmaa_session'].createJobTemplate()
jt.remoteCommand = '/bin/bash'
jt.args = args
jt.jobName = name
jt.errorPath = ':{}.err'.format(log_path)
jt.outputPath = ':{}.out'.format(log_path)
# pass execution parameters to job template
native_spec = ' --nodes=1 --ntasks=1'
if 'queue' in self._step['execution']['parameters']:
native_spec += ' -p {}'.format(
self._step['execution']['parameters']['queue'])
if 'slots' in self._step['execution']['parameters']:
native_spec += ' --cpus-per-task={}'.format(
self._step['execution']['parameters']['slots'])
if 'other' in self._step['execution']['parameters']:
native_spec += ' {}'.format(
self._step['execution']['parameters']['other'])
jt.nativeSpecification = native_spec
# submit hpc job using drmaa library
try:
job_id = self._slurm['drmaa_session'].runJob(jt)
except drmaa.DrmCommunicationException as err:
msg = 'cannot submit slurm job for step "{}" [{}]'\
.format(self._step['name'], str(err))
Log.a().warning(msg)
# set to failed, but return True so that it's retried
map_item['status'] = 'FAILED'
map_item['run'][map_item['attempt']]['status'] = 'FAILED'
return True
self._slurm['drmaa_session'].deleteJobTemplate(jt)
Log.a().debug('[step.%s]: hpc job id: %s -> %s', self._step['name'],
map_item['template']['output'], job_id)
# record job info
map_item['run'][map_item['attempt']]['hpc_job_id'] = job_id
# set status of process
map_item['status'] = 'QUEUED'
map_item['run'][map_item['attempt']]['status'] = 'QUEUED'
return True
def check_running_jobs(self):
"""
Check the status/progress of all map-reduce items..
And update _map status.
Args:
self: class instance.
Returns:
True.
"""
# check if jobs are still running
for map_item in self._map:
map_item['status'] = self._agave['agave_wrapper'].jobs_get_status(
map_item['run'][map_item['attempt']]['agave_job_id']
)
# for status failures, set to 'UNKNOWN'
if not map_item['status']:
msg = 'cannot get job status for step "{}"'\
.format(self._step['name'])
Log.a().warning(msg)
map_item['status'] = 'UNKNOWN'
# set status of run-attempt
map_item['run'][map_item['attempt']]['status'] = map_item['status']
# check hpc job ids
if map_item['run'][map_item['attempt']]['hpc_job_id']:
# already have it
continue
# job id listed in history
response = self._agave['agave_wrapper'].jobs_get_history(
map_item['run'][map_item['attempt']]['agave_job_id']
)
if not response:
msg = 'cannot get hpc job id for job: agave_job_id={}'.format(
map_item['run'][map_item['attempt']]['agave_job_id']
)
Log.a().warning(msg)
continue
for item in response:
if item['status'] == 'QUEUED':
match = re.match(
r'^HPC.*local job (\d*)$', item['description']
)
if match:
map_item['run'][map_item['attempt']]['hpc_job_id'] \
= match.group(1)
# log hpc job id
Log.some().debug(
'[step.%s]: hpc job id: %s -> %s',
self._step['name'],
map_item['template']['output'],
match.group(1)
)
break
if map_item['status'] == 'FAILED' and map_item['attempt'] < 5:
# retry job if not at limit
if not self.retry_failed(map_item):
Log.a().warning(
'[step.%s]: cannot retry failed agave job (%s)',
self._step['name'],
map_item['template']['output']
)
self._update_status_db(self._status, '')
return True
def check_running_jobs(self):
"""
Check the status/progress of all map-reduce items..
And update _map status.
Args:
self: class instance.
Returns:
True.
"""
# check if jobs are still running
for map_item in self._map:
if map_item['status'] not in ['FINISHED','FAILED','PENDING']:
map_item['status'] = self._agave['agave_wrapper'].jobs_get_status(
map_item['run'][map_item['attempt']]['agave_job_id']
)
# for status failures, set to 'UNKNOWN'
if not map_item['status']:
msg = 'cannot get job status for step "{}"'\
.format(self._step['name'])
Log.a().warning(msg)
map_item['status'] = 'UNKNOWN'
if map_item['status'] in ['FINISHED','FAILED']:
# status changed to finished or failed
Log.a().debug(
'[step.%s]: exit status: %s -> %s',
self._step['name'],
map_item['template']['output'],
map_item['status']
)
# decrease num running procs
if self._num_running > 0:
self._num_running -= 1
# check hpc job ids
if (
map_item['status'] != 'PENDING' \
and not map_item['run'][map_item['attempt']].get('hpc_job_id', '')
):
# job id listed in history
response = self._agave['agave_wrapper'].jobs_get_history(
map_item['run'][map_item['attempt']]['agave_job_id']
)
if not response:
msg = 'cannot get hpc job id for job: agave_job_id={}'.format(
map_item['run'][map_item['attempt']]['agave_job_id']
)
Log.a().warning(msg)
else:
for item in response:
if item['status'] == 'QUEUED':
match = re.match(
r'^HPC.*local job (\d*)$', item['description']
)
if match:
map_item['run'][map_item['attempt']]['hpc_job_id'] \
= match.group(1)
# log hpc job id
Log.some().debug(
'[step.%s]: hpc job id: %s -> %s',
self._step['name'],
map_item['template']['output'],
match.group(1)
)
break
map_item['run'][map_item['attempt']]['status'] = map_item['status']
if map_item['status'] == 'FAILED' and map_item['attempt'] < 5:
if self._throttle_limit == 0 or self._num_running < self._throttle_limit:
# retry job if not at retry or throttle limit
if not self.retry_failed(map_item):
Log.a().warning(
'[step.%s]: cannot retry failed agave job (%s)',
self._step['name'],
map_item['template']['output']
)
else:
self._num_running += 1
self._update_status_db(self._status, '')
return True
def run(args, other_args, subparser):
"""
Run GeneFlow workflow engine.
Args:
args.workflow_path: workflow definition or package directory.
args.job: path to job definition
Returns:
On success: True.
On failure: False.
"""
# get absolute path to workflow
workflow_path = resolve_workflow_path(args.workflow_path)
if workflow_path:
Log.some().info('workflow definition found: %s', workflow_path)
else:
Log.an().error('cannot find workflow definition: %s',
args.workflow_path)
return False
# setup environment
env = Environment(workflow_path=workflow_path)
if not env.initialize():
Log.an().error('cannot initialize geneflow environment')
return False
# create default config file and SQLite db
cfg = Config()
cfg.default(env.get_sqlite_db_path())
cfg.write(env.get_config_path())
config_dict = cfg.config('local')
# load workflow into db
try:
data_source = DataSource(config_dict['database'])
except DataSourceException as err:
Log.an().error('data source initialization error [%s]', str(err))
return False
defs = data_source.import_definition(workflow_path)
if not defs:
Log.an().error('workflow definition load failed: %s', workflow_path)
return False
if not defs['workflows']:
Log.an().error('workflow definition load failed: %s', workflow_path)
return False
data_source.commit()
for workflow in defs['workflows']:
Log.some().info('workflow loaded: %s -> %s', workflow,
defs['workflows'][workflow])
# get workflow definition back from database to ensure
# that it's a valid definition
workflow_id = next(iter(defs['workflows'].values()))
workflow_dict = data_source.get_workflow_def_by_id(workflow_id)
if not workflow_dict:
Log.an().error(
'cannot get workflow definition from data source: workflow_id=%s',
workflow_id)
return False
### define arg parsing methods
def parse_dynamic_args(workflow_dict):
"""
Parse dynamic args based on workflow dictionary as well as
some static args.
Args:
other_args: List of remaining args from initial parse of
workflow path.
workflow_dict: Workflow dictionary
Returns:
On success: List of parsed arguments.
On failure: False.
"""
# parse dynamic args. these are determined from workflow definition
dynamic_parser = argparse.ArgumentParser()
dynamic_parser.add_argument('-j',
'--job',
type=str,
default=None,
dest='job_path',
help='Job Definition(s)')
for input_key in workflow_dict['inputs']:
dynamic_parser.add_argument(
'--in.{}'.format(input_key),
dest='inputs.{}'.format(input_key),
required=False,
default=workflow_dict['inputs'][input_key]['default'],
help=workflow_dict['inputs'][input_key]['label'])
for param_key in workflow_dict['parameters']:
dynamic_parser.add_argument(
'--param.{}'.format(param_key),
dest='parameters.{}'.format(param_key),
required=False,
default=workflow_dict['parameters'][param_key]['default'],
help=workflow_dict['parameters'][param_key]['label'])
dynamic_parser.add_argument('-o',
'--output',
type=str,
default='~/geneflow-output',
help='Output Folder')
dynamic_parser.add_argument('-n',
'--name',
type=str,
default='geneflow-job',
help='Name of Job')
dynamic_parser.add_argument('-w',
'--work',
nargs='+',
type=str,
default=[],
help='Work Directory')
dynamic_parser.add_argument('--exec-context',
'--ec',
nargs='+',
type=str,
dest='exec_context',
default=[],
help='Execution Contexts')
dynamic_parser.add_argument('--exec-method',
'--em',
nargs='+',
type=str,
dest='exec_method',
default=[],
help='Execution Methods')
dynamic_parser.add_argument('--exec-param',
'--ep',
nargs='+',
type=str,
dest='exec_param',
default=[],
help='Execution Parameters')
dynamic_args = dynamic_parser.parse_known_args(other_args)
return dynamic_args[0]
if 'gooey' in sys.modules:
@Gooey(program_name='GeneFlow: {}'.format(workflow_dict['name']),
program_description=workflow_dict['description'],
target='gf --log-level={} run {}'.format(
args.log_level, args.workflow_path),
monospace_display=True)
def parse_dynamic_args_gui(workflow_dict):
"""
Parse dynamic args based on workflow dictionary as well as
some static args. Display a GUI interface.
Args:
other_args: List of remaining args from initial parse of
workflow path.
workflow_dict: Workflow dictionary
Returns:
On success: List of parsed arguments.
On failure: False.
"""
# parse dynamic args. these are determined from workflow definition
dynamic_parser = GooeyParser()
input_group = dynamic_parser.add_argument_group(
"Workflow Inputs",
"Files or folders to be passed to the workflow")
for input_key in workflow_dict['inputs']:
widget = 'FileChooser'
if workflow_dict['inputs'][input_key]['type'] == 'Directory':
widget = 'DirChooser'
input_group.add_argument(
'--in.{}'.format(input_key),
dest='inputs.{}'.format(input_key),
required=False,
default=workflow_dict['inputs'][input_key]['default'],
help=workflow_dict['inputs'][input_key]['label'],
widget=widget)
param_group = dynamic_parser.add_argument_group(
"Workflow Parameters",
"Number or string parameters to be passed to the workflow")
for param_key in workflow_dict['parameters']:
param_group.add_argument(
'--param.{}'.format(param_key),
dest='parameters.{}'.format(param_key),
required=False,
default=workflow_dict['parameters'][param_key]['default'],
help=workflow_dict['parameters'][param_key]['label'])
job_group = dynamic_parser.add_argument_group(
"Job Options", "Output/intermediate folders and job name")
job_group.add_argument('-o',
'--output',
type=str,
default='~/geneflow-output',
help='Output Folder',
widget='DirChooser')
job_group.add_argument('-n',
'--name',
type=str,
default='geneflow-job',
help='Name of Job')
job_group.add_argument('-w',
'--work',
nargs='+',
type=str,
default=[],
help='Work Directory')
exec_group = dynamic_parser.add_argument_group(
"Execution Options", "Customize workflow execution")
exec_group.add_argument('--exec-context',
'--ec',
nargs='+',
type=str,
dest='exec_context',
default=[],
help='Execution Contexts')
exec_group.add_argument('--exec-method',
'--em',
nargs='+',
type=str,
dest='exec_method',
default=[],
help='Execution Methods')
exec_group.add_argument('--exec-param',
'--ep',
nargs='+',
type=str,
dest='exec_param',
default=[],
help='Execution Parameters')
dynamic_args = dynamic_parser.parse_args(other_args)
return dynamic_args
# get dynamic args
if args.gui and 'gooey' in sys.modules:
dynamic_args = parse_dynamic_args_gui(workflow_dict)
else:
dynamic_args = parse_dynamic_args(workflow_dict)
# get absolute path to job file if provided
job_path = None
if dynamic_args.job_path:
job_path = Path(dynamic_args.job_path).absolute()
# load job definition if provided
jobs_dict = {}
gf_def = Definition()
if job_path:
if not gf_def.load(job_path):
Log.an().error('Job definition load failed')
return False
jobs_dict = gf_def.jobs()
else:
# create default definition
jobs_dict = {
'job': {
'name': 'GeneFlow job',
'output_uri': 'geneflow_output',
'work_uri': {
'local': '~/.geneflow/work'
}
}
}
# override with known cli parameters
apply_job_modifiers(jobs_dict, [
'name={}'.format(dynamic_args.name), 'output_uri={}'.format(
dynamic_args.output)
])
# insert workflow name into job, if not provided
workflow_name = next(iter(defs['workflows']))
for job in jobs_dict.values():
if 'workflow_name' not in job:
job['workflow_name'] = workflow_name
# add inputs and parameters to job definition
apply_job_modifiers(
jobs_dict,
[
'{}={}'.format(dynamic_arg, getattr(dynamic_args, dynamic_arg))
for dynamic_arg in vars(dynamic_args) \
if dynamic_arg.startswith('inputs.') or dynamic_arg.startswith('parameters.')
]
)
# add work URIs to job definition
work_uris = {}
for work_arg in dynamic_args.work:
parsed_work_uri = URIParser.parse(work_arg)
if not parsed_work_uri:
# skip if invalid URI
Log.a().warning('invalid work uri: %s', work_arg)
else:
work_uris[
parsed_work_uri['scheme']] = parsed_work_uri['chopped_uri']
apply_job_modifiers(jobs_dict, [
'work_uri.{}={}'.format(context, work_uris[context])
for context in work_uris
])
# add execution options to job definition
apply_job_modifiers(jobs_dict, [
'execution.context.{}={}'.format(*exec_arg.split(':', 1)[0:2])
for exec_arg in dynamic_args.exec_context
] + [
'execution.method.{}={}'.format(*exec_arg.split(':', 1)[0:2])
for exec_arg in dynamic_args.exec_method
] + [
'execution.parameters.{}={}'.format(*exec_arg.split(':', 1)[0:2])
for exec_arg in dynamic_args.exec_param
])
# get default values from workflow definition
for job in jobs_dict.values():
if 'inputs' not in job:
job['inputs'] = {}
if 'parameters' not in job:
job['parameters'] = {}
for input_key in workflow_dict['inputs']:
if input_key not in job['inputs']:
job['inputs'][input_key]\
= workflow_dict['inputs'][input_key]['default']
for param_key in workflow_dict['parameters']:
if param_key not in job['parameters']:
job['parameters'][param_key]\
= workflow_dict['parameters'][param_key]['default']
# expand URIs
for job in jobs_dict.values():
# output URI
parsed_uri = URIParser.parse(job['output_uri'])
if not parsed_uri:
Log.an().error('invalid output uri: %s', job['output_uri'])
return False
# expand relative path if local
if parsed_uri['scheme'] == 'local':
job['output_uri'] = str(
Path(parsed_uri['chopped_path']).expanduser().resolve())
# work URIs
for context in job['work_uri']:
parsed_uri = URIParser.parse(job['work_uri'][context])
if not parsed_uri:
Log.an().error('invalid work uri: %s', job['work_uri'])
return False
# expand relative path if local
if parsed_uri['scheme'] == 'local':
job['work_uri'][context] = str(
Path(parsed_uri['chopped_path']).expanduser().resolve())
# input URIs
for input_key in job['inputs']:
parsed_uri = URIParser.parse(job['inputs'][input_key])
if not parsed_uri:
Log.an().error('invalid input uri: %s',
job['inputs'][input_key])
return False
# expand relative path if local
if parsed_uri['scheme'] == 'local':
job['inputs'][input_key] = str(
Path(parsed_uri['chopped_path']).expanduser().resolve())
# import jobs into database
job_ids = data_source.import_jobs_from_dict(jobs_dict)
if job_ids is False:
Log.an().error('cannot import jobs')
return False
data_source.commit()
# create process pool to run workflows in parallel
pool = Pool(min(5, len(job_ids)))
jobs = [{'name': job, 'id': job_ids[job], 'log': None} for job in job_ids]
result = pool.map(
partial(geneflow.cli.common.run_workflow,
config=config_dict,
log_level=args.log_level), jobs)
pool.close()
pool.join()
if not all(result):
Log.an().error('some jobs failed')
return result
def run_pending(args):
"""
Run any jobs in database in the PENDING state.
Args:
args.config_file: GeneFlow config file path.
args.environment: Config environment.
Returns:
On success: True.
On failure: False.
"""
config_file = args.config_file
environment = args.environment
log_location = args.log_location
# load config file
cfg = Config()
if not cfg.load(config_file):
Log.an().error('cannot load config file: %s', config_file)
return False
config_dict = cfg.config(environment)
if not config_dict:
Log.an().error('invalid config environment: %s', environment)
return False
# connect to data source
try:
data_source = DataSource(config_dict['database'])
except DataSourceException as err:
Log.an().error('data source initialization error [%s]', str(err))
return False
# get pending jobs from database
pending_jobs = data_source.get_pending_jobs()
if pending_jobs is False:
Log.an().error('cannot query for pending jobs')
return False
if not pending_jobs:
# no jobs found
return True
Log.some().info('pending jobs found:\n%s', pprint.pformat(pending_jobs))
# set job status to QUEUED to minimize the chance that another
# process will try to run it
for job in pending_jobs:
if not data_source.update_job_status(job['id'], 'QUEUED', ''):
Log.a().warning('cannot update job status in data source')
data_source.rollback()
data_source.commit()
# create a thread pool to run at most 5 jobs concurrently
pool = Pool(min(5, len(pending_jobs)))
jobs = [{
'name': job['name'],
'id': job['id'],
'log': str(Path(log_location) / (job['id'] + '.log'))
} for job in pending_jobs]
result = pool.map(
partial(geneflow.cli.common.run_workflow,
config=config_dict,
log_level=args.log_level), jobs)
pool.close()
pool.join()
if not all(result):
Log.an().error('some jobs failed')
return result
