def initialize(self):
"""
Initialize the GeneFlow WorkflowInstaller class.
Initialize the class by cloning the workflow, validating the
structure, loading apps config, and connecting to agave.
Args:
self: class instance
Returns:
On success: True.
On failure: False.
"""
# clone workflow
if self._git:
if not self._clone_workflow():
Log.an().error('cannot clone workflow from %s', self._git)
return False
# validate workflow structure
if not self._validate_workflow_package():
Log.an().error('invalid workflow package at %s', self._path)
return False
# load workflow definition
if not self._load_workflow_def():
Log.an().error('cannot load workflow definition from %s', self._workflow_yaml)
return False
# connect to agave
if self._config and self._agave_params:
if self._config.get('agave') and self._agave_params.get('agave'):
self._config['agave']['token_username'] = self._agave_username
self._config['agave']['domain'] = self._agave_domain
self._agave_wrapper = AgaveWrapper(self._config['agave'])
if not self._agave_wrapper.connect():
Log.an().error('cannot connect to agave')
return False
return True
def __init__(self, config, job, parsed_job_work_uri):
"""
Initialize the GeneFlow AgaveWorkflow class.
Args:
self: class instance
config: GeneFlow config
job: job dictionary
parsed_job_work_uri: job work URI
Returns:
Class instance.
"""
self._job = job
self._config = config
self._parsed_job_work_uri = parsed_job_work_uri
# init agave wrapper object
self._agave_wrapper = AgaveWrapper(
config['agave'], token_username=self._job['username'])
self._parsed_archive_uri = None
class WorkflowInstaller:
"""
GeneFlow WorkflowInstaller class.
The WorkflowInstaller class is used to download and install workflows
from a GeneFlow git repo.
"""
def __init__(
self,
path,
git=None,
git_branch=None,
force=False,
app_name=None,
clean=False,
config=None,
agave_params=None,
agave_username=None,
agave_domain=None,
agave_publish=False,
make_apps=True
):
"""
Initialize the GeneFlow WorkflowInstaller class.
Args:
self: class instance
path: local path to the workflow package
git: git repo to clone
git_branch: branch or tag of git repo
force: delete existing folder before install?
app_name: name of app to install
clean: delete apps folder before install?
config: GeneFlow config dict that contains Agave client if needed
agave_params: dict that contains agave parameters for
app registration
agave_username: agave username to impersonate when installing apps
agave_publish: publish agave app?
make_apps: compile app templates
Returns:
None
"""
self._path = path
self._git = git
self._git_branch = git_branch
self._force = force
self._app_name = app_name
self._clean = clean
self._make_apps = make_apps
self._workflow_yaml = None
# agave-related member variables
self._agave_wrapper = None
self._config = config
self._agave_params = agave_params
self._agave_username = agave_username
self._agave_domain = agave_domain
self._agave_publish = agave_publish
def initialize(self):
"""
Initialize the GeneFlow WorkflowInstaller class.
Initialize the class by cloning the workflow, validating the
structure, loading apps config, and connecting to agave.
Args:
self: class instance
Returns:
On success: True.
On failure: False.
"""
# clone workflow
if self._git:
if not self._clone_workflow():
Log.an().error('cannot clone workflow from %s', self._git)
return False
# validate workflow structure
if not self._validate_workflow_package():
Log.an().error('invalid workflow package at %s', self._path)
return False
# load workflow definition
if not self._load_workflow_def():
Log.an().error('cannot load workflow definition from %s', self._workflow_yaml)
return False
# connect to agave
if self._config and self._agave_params:
if self._config.get('agave') and self._agave_params.get('agave'):
self._config['agave']['token_username'] = self._agave_username
self._config['agave']['domain'] = self._agave_domain
self._agave_wrapper = AgaveWrapper(self._config['agave'])
if not self._agave_wrapper.connect():
Log.an().error('cannot connect to agave')
return False
return True
def _validate_workflow_package(self):
package_path = Path(self._path)
if not Path(package_path).is_dir():
Log.an().error('workflow package path is not a directory: %s', package_path)
return False
self._workflow_yaml = Path(package_path / 'workflow.yaml')
if not self._workflow_yaml.is_file():
Log.an().error('missing workflow.yaml file in workflow package')
return False
return True
def _load_workflow_def(self):
# load geneflow definition file
gf_def = Definition()
if not gf_def.load(str(self._workflow_yaml)):
Log.an().error('invalid geneflow definition: %s', self._workflow_yaml)
return False
# make sure there is a workflow definition in the file
if not gf_def.workflows():
Log.an().error('no workflows in geneflow definition')
return False
# extract the workflow definition
self._workflow = next(iter(gf_def.workflows().values()))
return True
@classmethod
def _yaml_to_dict(cls, path):
# read yaml file
try:
with open(path, 'rU') as yaml_file:
yaml_data = yaml_file.read()
except IOError as err:
Log.an().warning('cannot read yaml file: %s [%s]', path, str(err))
return False
# convert to dict
try:
yaml_dict = yaml.safe_load(yaml_data)
except yaml.YAMLError as err:
Log.an().warning('invalid yaml file: %s [%s]', path, str(err))
return False
return yaml_dict
def _clone_workflow(self):
if not self._git:
Log.an().error('must specify a git url to clone workflow')
return False
if self._force:
# remove workflow folder if it exists
if Path(self._path).is_dir():
shutil.rmtree(self._path)
try:
if self._git_branch:
Repo.clone_from(
self._git, self._path, branch=self._git_branch,
config='http.sslVerify=false'
)
else:
Repo.clone_from(
self._git, self._path,
config='http.sslVerify=false'
)
except GitError as err:
Log.an().error(
'cannot clone git repo: %s [%s]', self._git, str(err)
)
return False
return True
def install_apps(self):
"""
Install apps for the workflow package.
Args:
self: class instance.
Returns:
None
"""
apps_path = Path(self._path) / '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._workflow['apps']:
if self._app_name == app or not self._app_name:
Log.some().info(
'app: %s:%s [%s]',
app,
self._workflow['apps'][app]['git'],
self._workflow['apps'][app]['version']
)
repo_path = apps_path / slugify(app, regex_pattern=r'[^-a-z0-9_]+')
# create AppInstaller instance
app_installer = AppInstaller(
str(repo_path),
{
'name': app,
**self._workflow['apps'][app]
}
)
# clone app into install location
if not app_installer.clone_git_repo():
Log.an().error('cannot clone app to %s', str(repo_path))
return False
if not app_installer.load_app():
Log.an().error('cannot load app config')
return False
if self._make_apps:
if not app_installer.make():
Log.an().error('cannot compile app templates')
return False
# register in Agave
if (
self._agave_wrapper
and self._agave_params
and self._agave_params.get('agave')
):
register_result = app_installer.register_agave_app(
self._agave_wrapper,
self._agave_params,
self._agave_publish
)
if not register_result:
Log.an().error(
'cannot register app "%s" in agave', app
)
return False
Log.some().info(
'registered agave app:\n%s',
pprint.pformat(register_result)
)
# update app definition with implementation section
if not app_installer.update_def(
agave={
'apps_prefix': self._agave_params['agave']['appsPrefix'],
'revision': register_result['revision']
}
):
Log.an().error(
'cannot update app "%s" definition',
app
)
return False
else:
# update app definition with implementation section
if not app_installer.update_def(agave=None):
Log.an().error(
'cannot update app "%s" definition',
app
)
return False
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_wrapper
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_wrapper': self._agave_wrapper
}
):
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_wrapper': self._agave_wrapper
}
):
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
class AgaveWorkflow:
"""GeneFlow workflow extension class to support Agave."""
def __init__(self, config, job, parsed_job_work_uri):
"""
Initialize the GeneFlow AgaveWorkflow class.
Args:
self: class instance
config: GeneFlow config
job: job dictionary
parsed_job_work_uri: job work URI
Returns:
Class instance.
"""
self._job = job
self._config = config
self._parsed_job_work_uri = parsed_job_work_uri
# init agave wrapper object
self._agave_wrapper = AgaveWrapper(
config['agave'], token_username=self._job['username'])
self._parsed_archive_uri = None
def initialize(self):
"""
Initialize the GeneFlow AgaveWorkflow class.
Initialize by connecting to Agave.
Args:
self: class instance
Returns:
On success: True.
On failure: False.
"""
if not self._agave_wrapper.connect():
Log.an().error('cannot connect to agave')
return False
return True
def init_data(self):
"""
Initialize any data specific to this context.
Create the archive URI in Agave.
Args:
self: class instance
Returns:
On success: True.
On failure: False.
"""
if not self._init_archive_uri():
Log.an().error('cannot create archive uri')
return False
return True
def _init_archive_uri(self):
"""
Initialize and validate Agave job archive URI.
Args:
None.
Returns:
On success: True.
On failure: False.
"""
if 'agave' not in self._parsed_job_work_uri:
Log.an().error('job work uri must include an agave context')
return False
# construct archive URI
self._parsed_archive_uri = URIParser.parse('{}/_agave_jobs'.format(
self._parsed_job_work_uri['agave']['chopped_uri']))
if not self._parsed_archive_uri:
Log.an().error('invalid job work uri: %s',
self._parsed_job_work_uri['agave'])
return False
# create URI
if not DataManager.mkdir(parsed_uri=self._parsed_archive_uri,
recursive=True,
agave=self.get_context_options()):
Log.an().error('cannot create agave archive uri: %s',
self._parsed_archive_uri['chopped_uri'])
return False
return True
def get_context_options(self):
"""
Return dict of options specific for this context.
Args:
None.
Returns:
Dict containing agave connection object and agave options.
"""
return {
'agave_wrapper': self._agave_wrapper,
'parsed_archive_uri': self._parsed_archive_uri
}