Source code for galaxy.tool_util.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):
    from_provided_metadata = asbool(kwargs.get("from_provided_metadata", False))
    discover_via = kwargs.get("discover_via", "tool_provided_metadata" if from_provided_metadata else "pattern")
    if discover_via == "tool_provided_metadata":
        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]    def to_dict(self):
        return {
            'discover_via': self.discover_via,
            'dbkey': self.default_dbkey,
            'format': self.default_ext,
            'visible': self.default_visible,
            'assign_primary_output': self.assign_primary_output,
            'directory': self.directory,
            'recurse': self.recurse,
        }


[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

[docs]    def to_dict(self):
        as_dict = super(FilePatternDatasetCollectionDescription, self).to_dict()
        as_dict.update({
            "sort_key": self.sort_key,
            "sort_comp": self.sort_comp,
            "pattern": self.pattern,
            "recurse": self.recurse,
        })
        return as_dict


DEFAULT_DATASET_COLLECTOR_DESCRIPTION = FilePatternDatasetCollectionDescription(
    default_dbkey=LEGACY_DEFAULT_DBKEY,
)