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Source code for galaxy.tools.parser.output_collection_def
""" This module define an abstract class for reasoning about Galaxy's
dataset collection after jobs are finished.
"""
from galaxy.util import asbool
from .util import is_dict
DEFAULT_EXTRA_FILENAME_PATTERN = r"primary_DATASET_ID_(?P<designation>[^_]+)_(?P<visible>[^_]+)_(?P<ext>[^_]+)(_(?P<dbkey>[^_]+))?"
DEFAULT_SORT_BY = "filename"
DEFAULT_SORT_COMP = "lexical"
# XML can describe custom patterns, but these literals describe named
# patterns that will be replaced.
NAMED_PATTERNS = {
"__default__": DEFAULT_EXTRA_FILENAME_PATTERN,
"__name__": r"(?P<name>.*)",
"__designation__": r"(?P<designation>.*)",
"__name_and_ext__": r"(?P<name>.*)\.(?P<ext>[^\.]+)?",
"__designation_and_ext__": r"(?P<designation>.*)\.(?P<ext>[^\._]+)?",
}
INPUT_DBKEY_TOKEN = "__input__"
LEGACY_DEFAULT_DBKEY = None # don't use __input__ for legacy default collection
[docs]def dataset_collector_descriptions_from_elem(elem, legacy=True):
primary_dataset_elems = elem.findall("discover_datasets")
num_discover_dataset_blocks = len(primary_dataset_elems)
if num_discover_dataset_blocks == 0 and legacy:
collectors = [DEFAULT_DATASET_COLLECTOR_DESCRIPTION]
else:
collectors = [dataset_collection_description(**e.attrib) for e in primary_dataset_elems]
return _validate_collectors(collectors)
[docs]def dataset_collector_descriptions_from_output_dict(as_dict):
discover_datasets_dicts = as_dict.get("discover_datasets", [])
if is_dict(discover_datasets_dicts):
discover_datasets_dicts = [discover_datasets_dicts]
dataset_collector_descriptions = dataset_collector_descriptions_from_list(discover_datasets_dicts)
return _validate_collectors(dataset_collector_descriptions)
def _validate_collectors(collectors):
num_discover_dataset_blocks = len(collectors)
if num_discover_dataset_blocks > 1:
for collector in collectors:
if collector.discover_via == "tool_provided_metadata":
raise Exception("Cannot specify more than one discover dataset condition if any of them specify tool_provided_metadata.")
return collectors
[docs]def dataset_collector_descriptions_from_list(discover_datasets_dicts):
return list(map(lambda kwds: dataset_collection_description(**kwds), discover_datasets_dicts))
[docs]def dataset_collection_description(**kwargs):
if asbool(kwargs.get("from_provided_metadata", False)):
for key in ["pattern", "sort_by"]:
if kwargs.get(key):
raise Exception("Cannot specify attribute [%s] if from_provided_metadata is True" % key)
return ToolProvidedMetadataDatasetCollection(**kwargs)
else:
return FilePatternDatasetCollectionDescription(**kwargs)
[docs]class DatasetCollectionDescription(object):
[docs] def __init__(self, **kwargs):
self.default_dbkey = kwargs.get("dbkey", INPUT_DBKEY_TOKEN)
self.default_ext = kwargs.get("ext", None)
if self.default_ext is None and "format" in kwargs:
self.default_ext = kwargs.get("format")
self.default_visible = asbool(kwargs.get("visible", None))
self.assign_primary_output = asbool(kwargs.get('assign_primary_output', False))
self.directory = kwargs.get("directory", None)
self.recurse = False
[docs]class ToolProvidedMetadataDatasetCollection(DatasetCollectionDescription):
discover_via = "tool_provided_metadata"
[docs]class FilePatternDatasetCollectionDescription(DatasetCollectionDescription):
discover_via = "pattern"
[docs] def __init__(self, **kwargs):
super(FilePatternDatasetCollectionDescription, self).__init__(**kwargs)
pattern = kwargs.get("pattern", "__default__")
self.recurse = asbool(kwargs.get("recurse", False))
if pattern in NAMED_PATTERNS:
pattern = NAMED_PATTERNS.get(pattern)
self.pattern = pattern
sort_by = kwargs.get("sort_by", DEFAULT_SORT_BY)
if sort_by.startswith("reverse_"):
self.sort_reverse = True
sort_by = sort_by[len("reverse_"):]
else:
self.sort_reverse = False
if "_" in sort_by:
sort_comp, sort_by = sort_by.split("_", 1)
assert sort_comp in ["lexical", "numeric"]
else:
sort_comp = DEFAULT_SORT_COMP
assert sort_by in [
"filename",
"name",
"designation",
"dbkey"
]
self.sort_key = sort_by
self.sort_comp = sort_comp
DEFAULT_DATASET_COLLECTOR_DESCRIPTION = FilePatternDatasetCollectionDescription(
default_dbkey=LEGACY_DEFAULT_DBKEY,
)