Commit 739b2e80 authored by davelopez's avatar davelopez
Browse files

Ensure `world` state before running some task 

- Add parameter to ensure_can_change_datatype and ensure_can_set_metadata to return a boolean instead of raising exceptions
- Check that we can perform the actions in the actual change_datatype and set_metadata celery tasks
parent 9e5fc9ea

lib/galaxy/celery/tasks.py

+19 −12
Original line number Diff line number Diff line
@@ -19,6 +19,7 @@ from galaxy.datatypes import sniff 
from galaxy.datatypes.registry import Registry as DatatypesRegistry

from galaxy.jobs import MinimalJobWrapper

from galaxy.managers.collections import DatasetCollectionManager

from galaxy.managers.datasets import DatasetAssociationManager

from galaxy.managers.hdas import HDAManager

from galaxy.managers.lddas import LDDAManager

from galaxy.managers.markdown_util import generate_branded_pdf
@@ -109,7 +110,12 @@ def change_datatype( 
    datatype: str,

    model_class: str = "HistoryDatasetAssociation",

):

    dataset_instance = _get_dataset_by_id(hda_manager, ldda_manager, dataset_id, model_class)

    manager = _get_dataset_manager(hda_manager, ldda_manager, model_class)

    dataset_instance = manager.by_id(dataset_id)

    can_change_datatype = manager.ensure_can_change_datatype(dataset_instance, raiseException=False)

    if not can_change_datatype:

        log.info(f"Changing datatype is not allowed for {model_class} {dataset_instance.id}")

        return

    if datatype == "auto":

        path = dataset_instance.dataset.file_name

        datatype = sniff.guess_ext(path, datatypes_registry.sniff_order)
@@ -127,10 +133,13 @@ def set_metadata( 
    model_class: str = "HistoryDatasetAssociation",

    overwrite: bool = True,

):

    dataset_instance = _get_dataset_by_id(hda_manager, ldda_manager, dataset_id, model_class)

    manager = _get_dataset_manager(hda_manager, ldda_manager, model_class)

    dataset_instance = manager.by_id(dataset_id)

    can_set_metadata = manager.ensure_can_set_metadata(dataset_instance, raiseException=False)

    if not can_set_metadata:

        log.info(f"Setting metadata is not allowed for {model_class} {dataset_instance.id}")

        return

    try:

        if dataset_instance.has_deferred_data:

            return  # Skip setting metadata on deferred datasets

        if overwrite:

            hda_manager.overwrite_metadata(dataset_instance)

        dataset_instance.datatype.set_meta(dataset_instance)
@@ -142,17 +151,15 @@ def set_metadata( 
    sa_session.flush()





def _get_dataset_by_id(

    hda_manager: HDAManager, ldda_manager: LDDAManager, dataset_id: int, model_class: str = "HistoryDatasetAssociation"

) -> model.DatasetInstance:

    dataset: model.DatasetInstance

def _get_dataset_manager(

    hda_manager: HDAManager, ldda_manager: LDDAManager, model_class: str = "HistoryDatasetAssociation"

) -> DatasetAssociationManager:

    if model_class == "HistoryDatasetAssociation":

        dataset = hda_manager.by_id(dataset_id)

        return hda_manager

    elif model_class == "LibraryDatasetDatasetAssociation":

        dataset = ldda_manager.by_id(dataset_id)

        return ldda_manager

    else:

        raise NotImplementedError(f"Cannot set metadata for model_class {model_class}")

    return dataset

        raise NotImplementedError(f"Cannot find manager for model_class {model_class}")





@galaxy_task(bind=True)

lib/galaxy/managers/datasets.py

+8 −2
Original line number Diff line number Diff line
@@ -382,17 +382,23 @@ class DatasetAssociationManager( 
            rval["modify_item_roles"] = modify_item_role_list

        return rval



    def ensure_can_change_datatype(self, dataset: model.DatasetInstance):

    def ensure_can_change_datatype(self, dataset: model.DatasetInstance, raiseException: bool = True) -> bool:

        if not dataset.datatype.is_datatype_change_allowed():

            if not raiseException:

                return False

            raise exceptions.InsufficientPermissionsException(

                f'Changing datatype "{dataset.extension}" is not allowed.'

            )

        return True



    def ensure_can_set_metadata(self, dataset: model.DatasetInstance):

    def ensure_can_set_metadata(self, dataset: model.DatasetInstance, raiseException: bool = True) -> bool:

        if not dataset.ok_to_edit_metadata():

            if not raiseException:

                return False

            raise exceptions.ItemAccessibilityException(

                "This dataset is currently being used as input or output. You cannot change datatype until the jobs have completed or you have canceled them."

            )

        return True



    def detect_datatype(self, trans, dataset_assoc):

        """Sniff and assign the datatype to a given dataset association (ldda or hda)"""