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[24.1] Extend on disk checks to running, queued and error states #18846

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Sep 19, 2024
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[24.1] Extend on disk checks to running, queued and error states #18846

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12 changes: 10 additions & 2 deletions lib/galaxy/managers/datasets.py
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Original file line number Diff line number Diff line change
Expand Up @@ -497,8 +497,8 @@ def ensure_dataset_on_disk(self, trans, dataset):
raise exceptions.ItemDeletionException("The dataset you are attempting to view has been deleted.")
elif dataset.state == Dataset.states.UPLOAD:
raise exceptions.Conflict("Please wait until this dataset finishes uploading before attempting to view it.")
elif dataset.state == Dataset.states.NEW:
raise exceptions.Conflict("The dataset you are attempting to view is new and has no data.")
elif dataset.state in (Dataset.states.NEW, Dataset.states.QUEUED):
raise exceptions.Conflict(f"The dataset you are attempting to view is {dataset.state} and has no data.")
elif dataset.state == Dataset.states.DISCARDED:
raise exceptions.ItemDeletionException("The dataset you are attempting to view has been discarded.")
elif dataset.state == Dataset.states.DEFERRED:
Expand All @@ -509,6 +509,14 @@ def ensure_dataset_on_disk(self, trans, dataset):
raise exceptions.Conflict(
"The dataset you are attempting to view is in paused state. One of the inputs for the job that creates this dataset has failed."
)
elif dataset.state == Dataset.states.RUNNING:
if not self.app.object_store.exists(dataset.dataset):
raise exceptions.Conflict(
"The dataset you are attempting to view is still being created and has no data yet."
)
elif dataset.state == Dataset.states.ERROR:
if not self.app.object_store.exists(dataset.dataset):
raise exceptions.RequestParameterInvalidException("The dataset is in error and has no data.")

def ensure_can_change_datatype(self, dataset: model.DatasetInstance, raiseException: bool = True) -> bool:
if not dataset.datatype.is_datatype_change_allowed():
Expand Down
24 changes: 1 addition & 23 deletions lib/galaxy/webapps/galaxy/controllers/dataset.py
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Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,6 @@
HDAManager,
)
from galaxy.managers.histories import HistoryManager
from galaxy.model import Dataset
from galaxy.model.base import transaction
from galaxy.model.item_attrs import (
UsesAnnotations,
Expand Down Expand Up @@ -108,33 +107,14 @@ def _check_dataset(self, trans, hda_id):
raise web.httpexceptions.HTTPNotFound(f"Invalid reference dataset id: {str(hda_id)}.")
if not self._can_access_dataset(trans, data):
return trans.show_error_message("You are not allowed to access this dataset")
if data.purged or data.dataset.purged:
return trans.show_error_message("The dataset you are attempting to view has been purged.")
elif data.deleted and not (trans.user_is_admin or (data.history and trans.get_user() == data.user)):
return trans.show_error_message("The dataset you are attempting to view has been deleted.")
elif data.state == Dataset.states.UPLOAD:
return trans.show_error_message(
"Please wait until this dataset finishes uploading before attempting to view it."
)
elif data.state == Dataset.states.DISCARDED:
return trans.show_error_message("The dataset you are attempting to view has been discarded.")
elif data.state == Dataset.states.DEFERRED:
return trans.show_error_message(
"The dataset you are attempting to view has deferred data. You can only use this dataset as input for jobs."
)
elif data.state == Dataset.states.PAUSED:
return trans.show_error_message(
"The dataset you are attempting to view is in paused state. One of the inputs for the job that creates this dataset has failed."
)
self.app.hda_manager.ensure_dataset_on_disk(trans, data)
return data

@web.expose
def display(
self, trans, dataset_id=None, preview=False, filename=None, to_ext=None, offset=None, ck_size=None, **kwd
):
data = self._check_dataset(trans, dataset_id)
if not isinstance(data, trans.app.model.DatasetInstance):
return data
if "hdca" in kwd:
raise RequestParameterInvalidException("Invalid request parameter 'hdca' encountered.")
if hdca_id := kwd.get("hdca_id", None):
Expand Down Expand Up @@ -478,8 +458,6 @@ def imp(self, trans, dataset_id=None, **kwd):
def display_by_username_and_slug(self, trans, username, slug, filename=None, preview=True, **kwargs):
"""Display dataset by username and slug; because datasets do not yet have slugs, the slug is the dataset's id."""
dataset = self._check_dataset(trans, slug)
if not isinstance(dataset, trans.app.model.DatasetInstance):
return dataset
# Filename used for composite types.
if filename:
return self.display(trans, dataset_id=slug, filename=filename)
Expand Down
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