def t_dataset(state, value, params):
"""
Incomplete
"""
if value:
tagPath = os.path.join(state.machineconf('dirs.tag_dir'), value)
if os.path.exists(tagPath):
# very cheap right now, move along nothing to see here
tagMetadata = json.loads(open(tagPath + '.metadata').read())
if 'urls' not in tagMetadata or ('urls' in tagMetadata and tagMetadata.get('urls_realized')):
if params.get('transform_type') == 'prefix':
# tagToRefDBPath basically does what prefix does
return defer.succeed(ptu.tagToRefDBPath(tagPath))
elif params.get('transform_type') == 'directory':
commonPrefix = ptu.tagToRefDBPath(tagPath)
if os.path.isdir(commonPrefix):
return defer.succeed(commonPrefix)
else:
return defer.succeed(os.path.dirname(commonPrefix))
elif params.get('transform_type') == 'tag_base_dir':
return defer.succeed(tagMetadata['tag_base_dir'])
else:
return defer.succeed(tagPath)
else:
return defer.succeed('undefined')
elif os.path.exists(tagPath + '.phantom'):
return defer.succeed('undefined')
else:
return defer.fail(InvalidPipelineValue('"%s" is not a valid tag' % str(value)))
else:
return defer.succeed('')
def t_dataset(state, value, params):
"""
Incomplete
"""
if value:
tagPath = os.path.join(state.machineconf('dirs.tag_dir'), value)
if os.path.exists(tagPath):
# very cheap right now, move along nothing to see here
tagMetadata = json.loads(open(tagPath + '.metadata').read())
if 'urls' not in tagMetadata or ('urls' in tagMetadata and
tagMetadata.get('urls_realized')):
if params.get('transform_type') == 'prefix':
# tagToRefDBPath basically does what prefix does
return defer.succeed(ptu.tagToRefDBPath(tagPath))
elif params.get('transform_type') == 'directory':
commonPrefix = ptu.tagToRefDBPath(tagPath)
if os.path.isdir(commonPrefix):
return defer.succeed(commonPrefix)
else:
return defer.succeed(os.path.dirname(commonPrefix))
elif params.get('transform_type') == 'tag_base_dir':
return defer.succeed(tagMetadata['tag_base_dir'])
else:
return defer.succeed(tagPath)
else:
return defer.succeed('undefined')
elif os.path.exists(tagPath + '.phantom'):
return defer.succeed('undefined')
else:
return defer.fail(
InvalidPipelineValue('"%s" is not a valid tag' % str(value)))
else:
return defer.succeed('')
def t_blastdb_dataset(state, value, _params):
"""
Incomplete
"""
if value:
tagPath = os.path.join(state.machineconf('dirs.tag_dir'), value)
if os.path.exists(tagPath):
# very cheap right now, move along nothing to see here
tagMetadata = json.loads(open(tagPath + '.metadata').read())
if 'urls' not in tagMetadata or ('urls' in tagMetadata and tagMetadata.get('urls_realized')):
return defer.succeed(ptu.tagToRefDBPath(tagPath))
else:
return defer.succeed('undefined')
elif os.path.exists(tagPath + '.phantom'):
return defer.succeed('undefined')
else:
return defer.fail(InvalidPipelineValue('"%s" is not a valid blastdb path' % str(value)))
else:
return defer.succeed('')
def t_blastdb_dataset(state, value, _params):
"""
Incomplete
"""
if value:
tagPath = os.path.join(state.machineconf('dirs.tag_dir'), value)
if os.path.exists(tagPath):
# very cheap right now, move along nothing to see here
tagMetadata = json.loads(open(tagPath + '.metadata').read())
if 'urls' not in tagMetadata or ('urls' in tagMetadata and
tagMetadata.get('urls_realized')):
return defer.succeed(ptu.tagToRefDBPath(tagPath))
else:
return defer.succeed('undefined')
elif os.path.exists(tagPath + '.phantom'):
return defer.succeed('undefined')
else:
return defer.fail(
InvalidPipelineValue('"%s" is not a valid blastdb path' %
str(value)))
else:
return defer.succeed('')