Warning

This document is for an old release of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

Source code for galaxy.sample_tracking.data_transfer

[docs]class DataTransferFactory(object): type = None
[docs] def parse(self): pass
[docs]class ScpDataTransferFactory(DataTransferFactory): type = 'scp'
[docs] def __init__(self): pass
[docs] def parse(self, config_file, elem): self.config = {} # TODO: The 'automatic_transfer' setting is for future use. If set to True, we will need to # ensure the sample has an associated destination data library before it moves to a certain state # ( e.g., Run started ). self.config['automatic_transfer'] = elem.get('automatic_transfer') self.config['host'] = elem.get('host') self.config['user_name'] = elem.get('user_name') self.config['password'] = elem.get('password') self.config['data_location'] = elem.get('data_location') # 'rename_dataset' is optional and it may not be defined in all external types # It is only used is AB SOLiD external service type for now rename_dataset = elem.get('rename_dataset', None) if rename_dataset: self.config['rename_dataset'] = rename_dataset # Validate for name, value in self.config.items(): assert value, "'%s' attribute missing in 'data_transfer' element of type 'scp' in external_service_type xml config file: '%s'." % (name, config_file)
[docs]class HttpDataTransferFactory(DataTransferFactory): type = 'http'
[docs] def __init__(self): pass
[docs] def parse(self, config_file, elem): self.config = {} self.config['automatic_transfer'] = elem.get('automatic_transfer') # Validate for name, value in self.config.items(): assert value, "'%s' attribute missing in 'data_transfer' element of type 'http' in external_service_type xml config file: '%s'." % (name, config_file)
[docs]class FtpDataTransferFactory(DataTransferFactory): type = 'ftp'
[docs] def __init__(self): pass
[docs] def parse(self, elem): pass
data_transfer_factories = dict([(data_transfer.type, data_transfer()) for data_transfer in [ScpDataTransferFactory, HttpDataTransferFactory, FtpDataTransferFactory]])