Unverified Commit e5fca086 authored by mvdbeek's avatar mvdbeek
Browse files

Assign default `data` extension on discovered collection output 

They used to be persisted as null in the database prior to this change.
parent dd171fe3

lib/galaxy/model/store/discover.py

+13 −7
Original line number Diff line number Diff line
@@ -38,6 +38,10 @@ from galaxy.util import ( 
from galaxy.util.hash_util import HASH_NAME_MAP



if TYPE_CHECKING:

    from galaxy.job_execution.output_collect import (

        DatasetCollector,

        ToolMetadataDatasetCollector,

    )

    from galaxy.model.store import ModelExportStore



log = logging.getLogger(__name__)
@@ -50,7 +54,7 @@ class MaxDiscoveredFilesExceededError(ValueError): 
    pass





CollectorT = Any  # TODO: setup an interface for these file collectors data classes.

CollectorT = Union["DatasetCollector", "ToolMetadataDatasetCollector"]





class ModelPersistenceContext(metaclass=abc.ABCMeta):
@@ -1056,19 +1060,21 @@ class JsonCollectedDatasetMatch: 
        return self.as_dict.get("name")



    @property

    def dbkey(self):

        return self.as_dict.get("dbkey", getattr(self.collector, "default_dbkey", "?"))

    def dbkey(self) -> str:

        return self.as_dict.get("dbkey", self.collector and self.collector.default_dbkey or "?")



    @property

    def ext(self):

        return self.as_dict.get("ext", getattr(self.collector, "default_ext", "data"))

    def ext(self) -> str:

        return self.as_dict.get("ext", self.collector and self.collector.default_ext or "data")



    @property

    def visible(self):

    def visible(self) -> bool:

        try:

            return self.as_dict["visible"].lower() == "visible"

        except KeyError:

            return getattr(self.collector, "default_visible", True)

            if self.collector and self.collector.default_visible is not None:

                return self.collector.default_visible

            return True



    @property

    def link_data(self):