def create_folder(cls, name, parent=None, project=None,
api=None):
"""Create a new folder
:param name: Folder name
:param parent: Parent folder
:param project: Project to create folder in
:param api: Api instance
:return: New folder
"""
api = api or cls._API
data = {
'name': name,
'type': cls.FOLDER_TYPE
}
if not parent and not project:
raise SbgError('Parent or project must be provided')
if parent and project:
raise SbgError(
'Providing both "parent" and "project" is not allowed'
)
if parent:
data['parent'] = Transform.to_file(file_=parent)
if project:
data['project'] = Transform.to_project(project=project)
response = api.post(url=cls._URL['create_folder'], data=data).json()
return cls(api=api, **response)
def query(cls,
project=None,
status=None,
batch=None,
parent=None,
offset=None,
limit=None,
api=None):
"""
Query (List) tasks
:param project: Target project. optional.
:param status: Task status.
:param batch: Only batch tasks.
:param parent: Parent batch task identifier.
:param offset: Pagination offset.
:param limit: Pagination limit.
:param api: Api instance.
:return: Collection object.
"""
api = api or cls._API
if parent:
parent = Transform.to_task(parent)
if project:
project = Transform.to_project(project)
return super(Task, cls)._query(url=cls._URL['query'],
project=project,
status=status,
batch=batch,
parent=parent,
offset=offset,
limit=limit,
fields='_all',
api=api)
def create_folder(cls, name, parent=None, project=None,
api=None):
"""Create a new folder
:param name: Folder name
:param parent: Parent folder
:param project: Project to create folder in
:param api: Api instance
:return: New folder
"""
api = api or cls._API
data = {
'name': name,
'type': cls.FOLDER_TYPE
}
if not parent and not project:
raise SbgError('Parent or project must be provided')
if parent and project:
raise SbgError(
'Providing both "parent" and "project" is not allowed'
)
if parent:
data['parent'] = Transform.to_file(file_=parent)
if project:
data['project'] = Transform.to_project(project=project)
response = api.post(url=cls._URL['create_folder'], data=data).json()
return cls(api=api, **response)
def submit_export(cls,
file,
volume,
location,
properties=None,
overwrite=False,
api=None):
"""
Submit new export job.
:param file: File to be exported.
:param volume: Volume identifier.
:param location: Volume location.
:param properties: Properties dictionary.
:param overwrite: If true it will overwrite file if exists
:param api: Api Instance.
:return: Export object.
"""
data = {}
volume = Transform.to_volume(volume)
file = Transform.to_file(file)
destination = {'volume': volume, 'location': location}
source = {'file': file}
if properties:
data['properties'] = properties
data['source'] = source
data['destination'] = destination
data['overwrite'] = overwrite
api = api if api else cls._API
_export = api.post(cls._URL['query'], data=data).json()
return Export(api=api, **_export)
def add(cls, user, permissions, automation, api=None):
"""
Add a member to the automation.
:param user: Member username
:param permissions: Permissions dictionary.
:param automation: Automation object or id
:param api: sevenbridges Api instance
:return: Automation member object.
"""
user = Transform.to_user(user)
automation = Transform.to_automation(automation)
api = api or cls._API
data = {'username': user}
if isinstance(permissions, dict):
data.update({
'permissions': permissions
})
member_data = api.post(
url=cls._URL['query'].format(automation_id=automation),
data=data
).json()
return AutomationMember(api=api, **member_data)
def query(cls,
project=None,
volume=None,
state=None,
offset=None,
limit=None,
api=None):
"""
Query (List) exports.
:param project: Optional project identifier.
:param volume: Optional volume identifier.
:param state: Optional import sate.
:param api: Api instance.
:return: Collection object.
"""
api = api or cls._API
if project:
project = Transform.to_project(project)
if volume:
volume = Transform.to_volume(volume)
return super(Export, cls)._query(url=cls._URL['query'],
project=project,
volume=volume,
state=state,
offset=offset,
limit=limit,
fields='_all',
api=api)
def submit_import(cls, volume, location, project, name=None,
overwrite=False, api=None):
"""
Submits new import job.
:param volume: Volume identifier.
:param location: Volume location.
:param project: Project identifier.
:param name: Optional file name.
:param overwrite: If true it will overwrite file if exists.
:param api: Api instance.
:return: Import object.
"""
data = {}
volume = Transform.to_volume(volume)
project = Transform.to_project(project)
source = {
'volume': volume,
'location': location
}
destination = {
'project': project
}
if name:
destination['name'] = name
data['source'] = source
data['destination'] = destination
data['overwrite'] = overwrite
api = api if api else cls._API
_import = api.post(cls._URL['query'], data=data).json()
return Import(api=api, **_import)
def upload(cls, path, project=None, parent=None, file_name=None,
overwrite=False, retry=5, timeout=10,
part_size=PartSize.UPLOAD_MINIMUM_PART_SIZE, wait=True,
api=None):
"""
Uploads a file using multipart upload and returns an upload handle
if the wait parameter is set to False. If wait is set to True it
will block until the upload is completed.
:param path: File path on local disc.
:param project: Project identifier
:param parent: Parent folder identifier
:param file_name: Optional file name.
:param overwrite: If true will overwrite the file on the server.
:param retry: Number of retries if error occurs during upload.
:param timeout: Timeout for http requests.
:param part_size: Part size in bytes.
:param wait: If true will wait for upload to complete.
:param api: Api instance.
"""
api = api or cls._API
extra = {'resource': cls.__name__, 'query': {
'path': path,
'project': project,
'file_name': file_name,
'overwrite': overwrite,
'retry': retry,
'timeout': timeout,
'part_size': part_size,
'wait': wait,
}}
logger.info('Uploading file', extra=extra)
if not project and not parent:
raise SbgError('A project or parent identifier is required.')
if project and parent:
raise SbgError(
'Project and parent identifiers are mutually exclusive.'
)
if project:
project = Transform.to_project(project)
if parent:
parent = Transform.to_file(parent)
upload = Upload(
file_path=path, project=project, parent=parent,
file_name=file_name, overwrite=overwrite, retry_count=retry,
timeout=timeout, part_size=part_size, api=api
)
if wait:
upload.start()
upload.wait()
return upload
else:
return upload
def upload(cls, path, project=None, parent=None, file_name=None,
overwrite=False, retry=5, timeout=60, part_size=None, wait=True,
api=None):
"""
Uploads a file using multipart upload and returns an upload handle
if the wait parameter is set to False. If wait is set to True it
will block until the upload is completed.
:param path: File path on local disc.
:param project: Project identifier
:param parent: Parent folder identifier
:param file_name: Optional file name.
:param overwrite: If true will overwrite the file on the server.
:param retry: Number of retries if error occurs during upload.
:param timeout: Timeout for http requests.
:param part_size: Part size in bytes.
:param wait: If true will wait for upload to complete.
:param api: Api instance.
"""
api = api or cls._API
extra = {'resource': cls.__name__, 'query': {
'path': path,
'project': project,
'file_name': file_name,
'overwrite': overwrite,
'retry': retry,
'timeout': timeout,
'part_size': part_size,
'wait': wait,
}}
logger.info('Uploading file', extra=extra)
if not project and not parent:
raise SbgError('A project or parent identifier is required.')
if project and parent:
raise SbgError(
'Project and parent identifiers are mutually exclusive.'
)
if project:
project = Transform.to_project(project)
if parent:
parent = Transform.to_file(parent)
upload = Upload(
file_path=path, project=project, parent=parent,
file_name=file_name, overwrite=overwrite, retry_count=retry,
timeout=timeout, part_size=part_size, api=api
)
if wait:
upload.start()
upload.wait()
return upload
else:
return upload
def bulk_submit(cls, imports, api=None):
"""
Submit imports in bulk
:param imports: List of dicts describing a wanted import.
:param api: Api instance.
:return: List of ImportBulkRecord objects.
"""
if not imports:
raise SbgError('Imports are required')
api = api or cls._API
items = []
for import_ in imports:
project = import_.get('project')
parent = import_.get('parent')
if project and parent:
raise SbgError(
'Project and parent identifiers are mutually exclusive')
elif project:
destination = {'project': Transform.to_project(project)}
elif parent:
destination = {'parent': Transform.to_file(parent)}
else:
raise SbgError('Project or parent identifier is required.')
volume = Transform.to_volume(import_.get('volume'))
location = Transform.to_location(import_.get('location'))
name = import_.get('name', None)
overwrite = import_.get('overwrite', False)
autorename = import_.get('autorename', None)
preserve_folder_structure = import_.get(
'preserve_folder_structure', None)
if name:
destination['name'] = name
import_config = {
'source': {
'volume': volume,
'location': location
},
'destination': destination,
'overwrite': overwrite,
}
if autorename is not None:
import_config['autorename'] = autorename
if preserve_folder_structure is not None:
import_config['preserve_folder_structure'] = (
preserve_folder_structure)
items.append(import_config)
data = {'items': items}
response = api.post(url=cls._URL['bulk_create'], data=data)
return ImportBulkRecord.parse_records(response=response, api=api)
def query(cls,
automation=None,
package=None,
status=None,
name=None,
created_by=None,
created_from=None,
created_to=None,
project_id=None,
order_by=None,
order=None,
offset=None,
limit=None,
api=None):
"""
Query (List) automation runs.
:param name: Automation run name
:param automation: Automation template
:param package: Package
:param status: Run status
:param created_by: Username of user that created the run
:param order_by: Property by which to order results
:param order: Ascending or descending ("asc" or "desc")
:param created_from: Date the run is created after
:param created_to: Date the run is created before
:param project_id: Id of project if Automation run is project based
:param offset: Pagination offset.
:param limit: Pagination limit.
:param api: Api instance.
:return: collection object
"""
if automation:
automation = Transform.to_automation(automation)
if package:
package = Transform.to_automation_package(package)
api = api or cls._API
return super()._query(
url=cls._URL['query'],
name=name,
automation_id=automation,
package_id=package,
status=status,
created_by=created_by,
created_from=created_from,
created_to=created_to,
project_id=project_id,
order_by=order_by,
order=order,
offset=offset,
limit=limit,
api=api,
)
def remove(cls, user, automation, api=None):
"""
Remove a member from the automation.
:param user: Member username
:param automation: Automation id
:param api: sevenbridges Api instance
:return: None
"""
user = Transform.to_user(user)
automation = Transform.to_automation(automation)
api = api or cls._API
api.delete(cls._URL['get'].format(automation_id=automation, id=user))
def submit_export(cls, file, volume, location, properties=None,
overwrite=False, copy_only=False, api=None):
"""
Submit new export job.
:param file: File to be exported.
:param volume: Volume identifier.
:param location: Volume location.
:param properties: Properties dictionary.
:param overwrite: If true it will overwrite file if exists
:param copy_only: If true files are kept on SevenBridges bucket.
:param api: Api Instance.
:return: Export object.
"""
data = {}
params = {}
volume = Transform.to_volume(volume)
file = Transform.to_file(file)
destination = {
'volume': volume,
'location': location
}
source = {
'file': file
}
if properties:
data['properties'] = properties
data['source'] = source
data['destination'] = destination
data['overwrite'] = overwrite
extra = {
'resource': cls.__name__,
'query': data
}
logger.info('Submitting export', extra=extra)
api = api if api else cls._API
if copy_only:
params['copy_only'] = True
_export = api.post(
cls._URL['query'], data=data, params=params).json()
else:
_export = api.post(
cls._URL['query'], data=data).json()
return Export(api=api, **_export)
def get(cls, id, automation, api=None):
"""
Fetches the resource from the server.
:param id: Automation member username
:param automation: Automation id or object
:param api: sevenbridges Api instance.
:return: AutomationMember object.
"""
username = Transform.to_resource(id)
automation = Transform.to_automation(automation)
api = api or cls._API
member = api.get(url=cls._URL['get'].format(automation_id=automation,
id=username)).json()
return AutomationMember(api=api, **member)
def create(cls, name, description=None, billing_group=None,
secret_settings=None, api=None):
"""
Create a automation template.
:param name: Automation name.
:param billing_group: Automation billing group.
:param description: Automation description.
:param secret_settings: Automation settings.
:param api: Api instance.
:return:
"""
api = api if api else cls._API
if name is None:
raise SbgError('Automation name is required!')
data = {
'name': name,
}
if billing_group:
data['billing_group'] = Transform.to_billing_group(billing_group)
if description:
data['description'] = description
if secret_settings:
data['secret_settings'] = secret_settings
extra = {
'resource': cls.__name__,
'query': data
}
logger.info('Creating automation template', extra=extra)
automation_data = api.post(url=cls._URL['query'], data=data).json()
return Automation(api=api, **automation_data)
def create(cls, file, name, position, chromosome, private=True, api=None):
"""
Create a marker on a file.
:param file: File object or identifier.
:param name: Marker name.
:param position: Marker position object.
:param chromosome: Chromosome number.
:param private: Whether the marker is private or public.
:param api: Api instance.
:return: Marker object.
"""
api = api if api else cls._API
file = Transform.to_file(file)
data = {
'file': file,
'name': name,
'position': position,
'chromosome': chromosome,
'private': private
}
extra = {
'resource': cls.__name__,
'query': data
}
logger.info('Creating marker', extra=extra)
marker_data = api.post(url=cls._URL['query'], data=data).json()
return Marker(api=api, **marker_data)
def create(cls, name, billing_group, description=None, tags=None,
api=None):
"""
Create a project.
:param name: Project name.
:param billing_group: Project billing group.
:param description: Project description.
:param tags: Project tags.
:param api: Api instance.
:return:
"""
api = api if api else cls._API
billing_group = Transform.to_billing_group(billing_group)
if name is None:
raise SbgError('Project name is required!')
data = {
'name': name,
'billing_group': billing_group,
}
if description:
data['description'] = description
if tags:
data['tags'] = tags
project_data = api.post(url=cls._URL['query'],
data=data).json()
return Project(api=api, **project_data)
def add_member(self, user, permissions):
"""
Add a member to the volume.
:param user: Member username
:param permissions: Permissions dictionary.
:return: Member object.
"""
user = Transform.to_user(user)
data = {'username': user, 'type': 'USER'}
if 'execute' in permissions:
permissions.pop('execute')
if isinstance(permissions, dict):
data.update({'permissions': permissions})
extra = {
'resource': type(self).__name__,
'query': {
'id': self.id,
'data': data,
}
}
logger.info('Adding volume member', extra=extra)
response = self._api.post(
url=self._URL['members_query'].format(id=self.id), data=data)
member_data = response.json()
return Member(api=self._api, **member_data)
def add_member_team(self, team, permissions):
"""
Add a member (team) to a volume.
:param team: Team object or team identifier.
:param permissions: Permissions dictionary.
:return: Member object.
"""
team = Transform.to_team(team)
data = {'id': team, 'type': 'TEAM'}
if 'execute' in permissions:
permissions.pop('execute')
if isinstance(permissions, dict):
data.update({'permissions': permissions})
extra = {
'resource': self.__class__.__name__,
'query': {
'id': self.id,
'data': data,
}
}
logger.info('Adding volume team member using team id', extra=extra)
response = self._api.post(
url=self._URL['members_query'].format(id=self.id), data=data)
member_data = response.json()
return Member(api=self._api, **member_data)
def add_member_team(self, team, permissions):
"""
Add a member (team) to a volume.
:param team: Team object or team identifier.
:param permissions: Permissions dictionary.
:return: Member object.
"""
team = Transform.to_team(team)
data = {'id': team, 'type': 'TEAM'}
if 'execute' in permissions:
permissions.pop('execute')
if isinstance(permissions, dict):
data.update({
'permissions': permissions
})
extra = {
'resource': self.__class__.__name__,
'query': {
'id': self.id,
'data': data,
}
}
logger.info('Adding volume team member using team id', extra=extra)
response = self._api.post(
url=self._URL['members_query'].format(id=self.id), data=data)
member_data = response.json()
return Member(api=self._api, **member_data)
def query(cls, division, offset=None, limit=None, api=None):
division = Transform.to_division(division)
api = api if api else cls._API
return super(Team, cls)._query(
url=cls._URL['query'], division=division, offset=offset,
limit=limit, fields='_all', api=api
)
def add_member(self, user, permissions):
"""
Add a member to the project.
:param user: Member username
:param permissions: Permissions dictionary.
:return: Member object.
"""
user = Transform.to_user(user)
data = {'username': user, 'type': 'USER'}
if isinstance(permissions, dict):
data.update({
'permissions': permissions
})
extra = {
'resource': self.__class__.__name__,
'query': {
'id': self.id,
'data': data,
}
}
logger.info('Adding member using username', extra=extra)
response = self._api.post(
url=self._URL['members_query'].format(id=self.id), data=data)
member_data = response.json()
return Member(api=self._api, **member_data)
def add_member_division(self, division, permissions):
"""
Add a member (team) to a project.
:param division: Division object or division identifier.
:param permissions: Permissions dictionary.
:return: Member object.
"""
division = Transform.to_division(division)
data = {'id': division, 'type': 'DIVISION'}
if isinstance(permissions, dict):
data.update({
'permissions': permissions
})
extra = {
'resource': self.__class__.__name__,
'query': {
'id': self.id,
'data': data,
}
}
logger.info('Adding team member using division id', extra=extra)
response = self._api.post(
url=self._URL['members_query'].format(id=self.id), data=data)
member_data = response.json()
return Member(api=self._api, **member_data)
def add_member_division(self, division, permissions):
"""
Add a member (team) to a volume.
:param division: Division object or division identifier.
:param permissions: Permissions dictionary.
:return: Member object.
"""
division = Transform.to_division(division)
if 'execute' in permissions:
permissions.pop('execute')
data = {'username': division, 'type': 'DIVISION'}
if isinstance(permissions, dict):
data.update({'permissions': permissions})
extra = {
'resource': type(self).__name__,
'query': {
'id': self.id,
'data': data,
}
}
logger.info('Adding volume division member', extra=extra)
response = self._api.post(
url=self._URL['members_query'].format(id=self.id), data=data)
member_data = response.json()
return Member(api=self._api, **member_data)
def create(cls, name, billing_group, description=None, tags=None,
api=None):
"""
Create a project.
:param name: Project name.
:param billing_group: Project billing group.
:param description: Project description.
:param tags: Project tags.
:param api: Api instance.
:return:
"""
api = api if api else cls._API
billing_group = Transform.to_billing_group(billing_group)
if name is None:
raise SbgError('Project name is required!')
data = {
'name': name,
'billing_group': billing_group,
}
if description:
data['description'] = description
if tags:
data['tags'] = tags
project_data = api.post(url=cls._URL['query'],
data=data).json()
return Project(api=api, **project_data)
def upload(cls, path, project, file_name=None, overwrite=False, retry=5,
timeout=10, part_size=PartSize.UPLOAD_MINIMUM_PART_SIZE,
wait=True, api=None):
"""
Uploads a file using multipart upload and returns an upload handle
if the wait parameter is set to False. If wait is set to True it
will block until the upload is completed.
:param path: File path on local disc.
:param project: Project identifier
:param file_name: Optional file name.
:param overwrite: If true will overwrite the file on the server.
:param retry: Number of retries if error occurs during upload.
:param timeout: Timeout for http requests.
:param part_size: Part size in bytes.
:param wait: If true will wait for upload to complete.
:param api: Api instance.
"""
api = api or cls._API
project = Transform.to_project(project)
upload = Upload(
path, project, file_name=file_name, overwrite=overwrite,
retry_count=retry, timeout=timeout, part_size=part_size, api=api
)
if wait:
upload.start()
upload.wait()
return upload
else:
return upload
def create(cls, file, name, position, chromosome, private=True, api=None):
"""
Create a marker on a file.
:param file: File object or identifier.
:param name: Marker name.
:param position: Marker position object.
:param chromosome: Chromosome number.
:param private: Whether the marker is private or public.
:param api: Api instance.
:return: Marker object.
"""
api = api if api else cls._API
file = Transform.to_file(file)
data = {
'file': file,
'name': name,
'position': position,
'chromosome': chromosome,
'private': private
}
extra = {'resource': cls.__name__, 'query': data}
logger.info('Creating marker', extra=extra)
marker_data = api.post(url=cls._URL['query'], data=data).json()
return Marker(api=api, **marker_data)
def query(cls,
project=None,
visibility=None,
q=None,
id=None,
offset=None,
limit=None,
api=None):
"""
Query (List) apps.
:param project: Source project.
:param visibility: private|public for private or public apps.
:param q: List containing search terms.
:param id: List contains app ids. Fetch apps with specific ids.
:param offset: Pagination offset.
:param limit: Pagination limit.
:param api: Api instance.
:return: collection object
"""
if project:
project = Transform.to_project(project)
api = api or cls._API
return super(App, cls)._query(url=cls._URL['query'],
project=project,
visibility=visibility,
q=q,
id=id,
offset=offset,
limit=limit,
api=api)
def remove_member(self, user):
"""
Remove member from the project.
:param user: User to be removed.
"""
member = Transform.to_user(user)
self._api.delete(
url=self._URL['members_get'].format(id=self.id, member=member))
def submit_export(cls,
file,
volume,
location,
properties=None,
overwrite=False,
copy_only=False,
api=None):
"""
Submit new export job.
:param file: File to be exported.
:param volume: Volume identifier.
:param location: Volume location.
:param properties: Properties dictionary.
:param overwrite: If true it will overwrite file if exists
:param copy_only: If true files are kept on SevenBridges bucket.
:param api: Api Instance.
:return: Export object.
"""
data = {}
params = {}
volume = Transform.to_volume(volume)
file = Transform.to_file(file)
destination = {'volume': volume, 'location': location}
source = {'file': file}
if properties:
data['properties'] = properties
data['source'] = source
data['destination'] = destination
data['overwrite'] = overwrite
extra = {'resource': cls.__name__, 'query': data}
logger.info('Submitting export', extra=extra)
api = api if api else cls._API
if copy_only:
params['copy_only'] = True
_export = api.post(cls._URL['query'], data=data,
params=params).json()
else:
_export = api.post(cls._URL['query'], data=data).json()
return Export(api=api, **_export)
def remove_member(self, user):
"""
Remove member from the project.
:param user: User to be removed.
"""
member = Transform.to_user(user)
self._api.delete(url=self._URL['members_get'].format(
id=self.id,
member=member))
def get_package(cls, package, api=None):
"""
Return specified automation member
:param package: Automation Package Id
:param api: sevenbridges Api instance.
:return: AutomationMember object
"""
package_id = Transform.to_automation_package(package)
api = api or cls._API
return AutomationPackage.get(id=package_id, api=api)
def get_member(self, username, api=None):
"""
Return specified automation member
:param username: Member username
:param api: sevenbridges Api instance.
:return: AutomationMember object
"""
member = Transform.to_automation_member(username)
api = api or self._API
return AutomationMember.get(id=member, automation=self.id, api=api)
def query(cls,
project,
names=None,
metadata=None,
origin=None,
tags=None,
offset=None,
limit=None,
api=None):
"""
Query ( List ) projects
:param project: Project id
:param names: Name list
:param metadata: Metadata query dict
:param origin: Origin query dict
:param tags: List of tags to filter on
:param offset: Pagination offset
:param limit: Pagination limit
:param api: Api instance.
:return: Collection object.
"""
api = api or cls._API
project = Transform.to_project(project)
query_params = {}
if names is not None and isinstance(names, list):
if len(names) == 0:
names.append("")
query_params['name'] = names
metadata_params = {}
if metadata and isinstance(metadata, dict):
for k, v in metadata.items():
metadata_params['metadata.' + k] = metadata[k]
if tags:
query_params['tag'] = tags
query_params.update(metadata_params)
origin_params = {}
if origin and isinstance(origin, dict):
for k, v in origin.items():
origin_params['origin.' + k] = origin[k]
query_params.update(origin_params)
return super(File, cls)._query(api=api,
url=cls._URL['query'],
project=project,
offset=offset,
limit=limit,
fields='_all',
**query_params)
def bulk_submit(cls, exports, copy_only=False, api=None):
"""
Create exports in bulk.
:param exports: List of dicts describing a wanted export.
:param copy_only: If true files are kept on SevenBridges bucket.
:param api: Api instance.
:return: list of ExportBulkRecord objects.
"""
if not exports:
raise SbgError('Exports are required')
api = api or cls._API
items = []
for export in exports:
file_ = Transform.to_file(export.get('file'))
volume = Transform.to_volume(export.get('volume'))
location = Transform.to_location(export.get('location'))
properties = export.get('properties', {})
overwrite = export.get('overwrite', False)
item = {
'source': {
'file': file_
},
'destination': {
'volume': volume,
'location': location
},
'properties': properties,
'overwrite': overwrite
}
items.append(item)
data = {'items': items}
params = {'copy_only': copy_only}
response = api.post(url=cls._URL['bulk_create'],
params=params,
data=data)
return ExportBulkRecord.parse_records(response=response, api=api)
def bulk_submit(cls, exports, copy_only=False, api=None):
"""
Create exports in bulk.
:param exports: Exports to be submitted in bulk.
:param copy_only: If true files are kept on SevenBridges bucket.
:param api: Api instance.
:return: list of ExportBulkRecord objects.
"""
if not exports:
raise SbgError('Exports are required')
api = api or cls._API
items = []
for export in exports:
file_ = Transform.to_file(export.get('file'))
volume = Transform.to_volume(export.get('volume'))
location = Transform.to_location(export.get('location'))
properties = export.get('properties', {})
overwrite = export.get('overwrite', False)
item = {
'source': {
'file': file_
},
'destination': {
'volume': volume,
'location': location
},
'properties': properties,
'overwrite': overwrite
}
items.append(item)
data = {'items': items}
params = {'copy_only': copy_only}
response = api.post(
url=cls._URL['bulk_create'], params=params, data=data
)
return ExportBulkRecord.parse_records(response=response, api=api)
def remove_member(self, member, api=None):
"""Remove member from a dataset
:param member: Member username
:param api: Api instance
:return: None
"""
api = api or self._API
username = Transform.to_member(member)
api.delete(
url=self._URL['member'].format(id=self.id, username=username))
def get_file_delete_job(cls, id, api=None):
"""
:param id: Async job identifier
:param api: Api instance
:return:
"""
id = Transform.to_async_job(id)
api = api if api else cls._API
async_job = api.get(url=cls._URL['get_file_delete_job'].format(
id=id)).json()
return AsyncJob(api=api, **async_job)
def bulk_submit(cls, imports, api=None):
"""
Submit imports in bulk
:param imports: Imports to be retrieved.
:param api: Api instance.
:return: List of ImportBulkRecord objects.
"""
if not imports:
raise SbgError('Imports are required')
api = api or cls._API
items = []
for import_ in imports:
volume = Transform.to_volume(import_.get('volume'))
location = Transform.to_location(import_.get('location'))
project = Transform.to_project(import_.get('project'))
name = import_.get('name', None)
overwrite = import_.get('overwrite', False)
item = {
'source': {
'volume': volume,
'location': location
},
'destination': {
'project': project
},
'overwrite': overwrite
}
if name:
item['destination']['name'] = name
items.append(item)
data = {'items': items}
response = api.post(url=cls._URL['bulk_create'], data=data)
return ImportBulkRecord.parse_records(response=response, api=api)
def get_file_delete_job(cls, id, api=None):
"""
:param id: Async job identifier
:param api: Api instance
:return:
"""
id = Transform.to_async_job(id)
api = api if api else cls._API
async_job = api.get(
url=cls._URL['get_file_delete_job'].format(id=id)
).json()
return AsyncJob(api=api, **async_job)
def bulk_get(cls, exports, api=None):
"""
Retrieve exports in bulk.
:param exports: Exports to be retrieved.
:param api: Api instance.
:return: list of ExportBulkRecord objects.
"""
api = api or cls._API
export_ids = [Transform.to_export(export) for export in exports]
data = {'export_ids': export_ids}
response = api.post(url=cls._URL['bulk_get'], data=data)
return ExportBulkRecord.parse_records(response=response, api=api)
def bulk_get(cls, exports, api=None):
"""
Retrieve exports in bulk.
:param exports: Exports to be retrieved.
:param api: Api instance.
:return: list of ExportBulkRecord objects.
"""
api = api or cls._API
export_ids = [Transform.to_export(export) for export in exports]
data = {'export_ids': export_ids}
response = api.post(url=cls._URL['bulk_get'], data=data)
return ExportBulkRecord.parse_records(response=response, api=api)
def bulk_delete(cls, files, api=None):
"""
Delete files with specified ids in bulk
:param files: Files to be deleted.
:param api: Api instance.
:return: List of FileBulkRecord objects.
"""
api = api or cls._API
file_ids = [Transform.to_file(file_) for file_ in files]
data = {'file_ids': file_ids}
logger.info('Deleting files in bulk.')
response = api.post(url=cls._URL['bulk_delete'], data=data)
return FileBulkRecord.parse_records(response=response, api=api)
def remove_member(self, member, api=None):
"""Remove member from a dataset
:param member: Member username
:param api: Api instance
:return: None
"""
api = api or self._API
username = Transform.to_member(member)
api.delete(
url=self._URL['member'].format(
id=self.id,
username=username
)
)
def copy(self, project, name=None):
"""
Copies the current file.
:param project: Destination project.
:param name: Destination file name.
:return: Copied File object.
"""
project = Transform.to_project(project)
data = {
'project': project
}
if name:
data['name'] = name
new_file = self._api.post(url=self._URL['copy'].format(id=self.id),
data=data).json()
return File(api=self._api, **new_file)
def query(cls, file, offset=None, limit=None, api=None):
"""
Queries genome markers on a file.
:param file: Genome file - Usually bam file.
:param offset: Pagination offset.
:param limit: Pagination limit.
:param api: Api instance.
:return: Collection object.
"""
api = api if api else cls._API
file = Transform.to_file(file)
return super(Marker, cls)._query(
url=cls._URL['query'], offset=offset, limit=limit,
file=file, fields='_all', api=api
)
def get(cls, id, api=None):
"""
Fetches the resource from the server.
:param id: Resource identifier
:param api: sevenbridges Api instance.
:return: Resource object.
"""
id = Transform.to_resource(id)
api = api if api else cls._API
if 'get' in cls._URL:
extra = {'resource': cls.__name__, 'query': {'id': id}}
logger.info('Fetching {} resource'.format(cls), extra=extra)
resource = api.get(url=cls._URL['get'].format(id=id)).json()
return cls(api=api, **resource)
else:
raise SbgError('Unable to fetch resource!')
def remove_member(self, user):
"""
Remove member from the project.
:param user: User to be removed.
"""
username = Transform.to_user(user)
extra = {
'resource': self.__class__.__name__,
'query': {
'id': self.id,
'user': user,
}
}
logger.info('Removing member', extra=extra)
self._api.delete(
url=self._URL['member'].format(id=self.id, username=username)
)
def query(cls, project=None, visibility=None, offset=None, limit=None,
api=None):
"""
Query (List) apps.
:param visibility:
:param project:
:param offset: Pagination offset.
:param limit: Pagination limit.
:param api: Api instance.
:return: collection object
"""
if project:
project = Transform.to_project(project)
api = api or cls._API
return super(App, cls)._query(url=cls._URL['query'], project=project,
visibility=visibility,
offset=offset, limit=limit, api=api)
def add_member(self, user, permissions):
"""
Add a member to the project.
:param user: Member username
:param permissions: Permissions dictionary.
:return: Member object.
"""
user = Transform.to_user(user)
data = {}
if isinstance(permissions, dict):
data = {
'username': user,
'permissions': permissions
}
response = self._api.post(
url=self._URL['members_query'].format(id=self.id), data=data)
member_data = response.json()
return Member(api=self._api, **member_data)
def copy(self, project, name=None):
"""
Copies the current app.
:param project: Destination project.
:param name: Destination app name.
:return: Copied App object.
"""
project = Transform.to_project(project)
data = {
'project': project
}
if name:
data['name'] = name
app = self._api.post(url=self._URL['copy'].format(id=self.id),
data=data).json()
return App(api=self._api, **app)
def query(cls, volume=None, state=None, offset=None,
limit=None, api=None):
"""
Query (List) exports.
:param volume: Optional volume identifier.
:param state: Optional import sate.
:param api: Api instance.
:return: Collection object.
"""
api = api or cls._API
if volume:
volume = Transform.to_volume(volume)
return super(Export, cls)._query(
url=cls._URL['query'], volume=volume, state=state, offset=offset,
limit=limit, fields='_all', api=api
)
def query(cls, project=None, visibility=None, q=None, id=None, offset=None,
limit=None, api=None):
"""
Query (List) apps.
:param project: Source project.
:param visibility: private|public for private or public apps.
:param q: List containing search terms.
:param id: List contains app ids. Fetch apps with specific ids.
:param offset: Pagination offset.
:param limit: Pagination limit.
:param api: Api instance.
:return: collection object
"""
if project:
project = Transform.to_project(project)
api = api or cls._API
return super(App, cls)._query(url=cls._URL['query'], project=project,
visibility=visibility, q=q, id=id,
offset=offset, limit=limit, api=api)
def bulk_copy_files(cls, files, destination_project, api=None):
"""
Bulk copy of files.
:param files: List containing files to be copied.
:param destination_project: Destination project.
:param api: Api instance.
:return: MultiStatus copy result.
"""
api = api if api else cls._API
files = [Transform.to_file(file) for file in files]
data = {
'project': destination_project,
'file_ids': files
}
extra = {
'resource': cls.__name__,
'query': data
}
logger.info('Performing bulk copy', extra=extra)
return api.post(url=cls._URL['bulk_copy'], data=data).json()
def query(cls, project=None, status=None, batch=None,
parent=None, offset=None, limit=None, api=None):
"""
Query (List) tasks
:param project: Target project. optional.
:param status: Task status.
:param batch: Only batch tasks.
:param parent: Parent batch task identifier.
:param offset: Pagination offset.
:param limit: Pagination limit.
:param api: Api instance.
:return: Collection object.
"""
api = api or cls._API
if parent:
parent = Transform.to_task(parent)
return super(Task, cls)._query(url=cls._URL['query'], project=project,
status=status, batch=batch,
parent=parent, offset=offset,
limit=limit, api=api)
def copy(self, project, name=None):
"""
Copies the current file.
:param project: Destination project.
:param name: Destination file name.
:return: Copied File object.
"""
project = Transform.to_project(project)
data = {
'project': project
}
if name:
data['name'] = name
extra = {'resource': self.__class__.__name__, 'query': {
'id': self.id,
'data': data
}}
logger.info('Copying file', extra=extra)
new_file = self._api.post(url=self._URL['copy'].format(id=self.id),
data=data).json()
return File(api=self._api, **new_file)
def add_member(self, user):
"""
Add member to team
:param user: User object or user's username
:return: Added user.
"""
user = Transform.to_user(user)
data = {
'id': user
}
extra = {
'resource': self.__class__.__name__,
'query': {
'id': self.id,
'data': data,
}
}
logger.info('Adding team member using id', extra=extra)
response = self._api.post(
url=self._URL['members_query'].format(id=self.id), data=data)
member_data = response.json()
return TeamMember(api=self._api, **member_data)
def create(cls, name, billing_group=None, description=None, tags=None,
settings=None, api=None):
"""
Create a project.
:param name: Project name.
:param billing_group: Project billing group.
:param description: Project description.
:param tags: Project tags.
:param settings: Project settings.
:param api: Api instance.
:return:
"""
api = api if api else cls._API
if name is None:
raise SbgError('Project name is required!')
data = {
'name': name,
}
if billing_group:
data['billing_group'] = Transform.to_billing_group(billing_group)
if description:
data['description'] = description
if tags:
data['tags'] = tags
if settings:
data['settings'] = settings
extra = {
'resource': cls.__name__,
'query': data
}
logger.info('Creating project', extra=extra)
project_data = api.post(url=cls._URL['create'], data=data).json()
return Project(api=api, **project_data)
def query(cls, project, names=None, metadata=None, origin=None,
offset=None, limit=None, api=None):
"""
Query ( List ) projects
:param project: Project id
:param names: Name list
:param metadata: Metadata query dict
:param origin: Origin query dict
:param offset: Pagination offset
:param limit: Pagination limit
:param api: Api instance.
:return: Collection object.
"""
api = api or cls._API
project = Transform.to_project(project)
query_params = {}
if names and isinstance(names, list):
query_params['name'] = names
metadata_params = {}
if metadata and isinstance(metadata, dict):
for k, v in metadata.items():
metadata_params['metadata.' + k] = metadata[k]
query_params.update(metadata_params)
origin_params = {}
if origin and isinstance(origin, dict):
for k, v in origin.items():
origin_params['origin.' + k] = origin[k]
query_params.update(origin_params)
return super(File, cls)._query(api=api, url=cls._URL['query'],
project=project, offset=offset,
limit=limit, **query_params)
