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('')