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Drop unused datasets controller methods #18568

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Jul 20, 2024
Merged

Drop unused datasets controller methods #18568

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274 changes: 0 additions & 274 deletions lib/galaxy/webapps/galaxy/controllers/dataset.py
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Original file line number Diff line number Diff line change
Expand Up @@ -42,11 +42,8 @@
from galaxy.util.sanitize_html import sanitize_html
from galaxy.util.zipstream import ZipstreamWrapper
from galaxy.web import form_builder
from galaxy.web.framework.helpers import iff
from galaxy.webapps.base.controller import (
BaseUIController,
ERROR,
SUCCESS,
url_for,
UsesExtendedMetadataMixin,
)
Expand Down Expand Up @@ -454,28 +451,6 @@ def _get_dataset_for_edit(self, trans, dataset_id):
trans.app.security_agent.set_dataset_permission(data.dataset, permissions)
return data, None

@web.expose
def imp(self, trans, dataset_id=None, **kwd):
"""Import another user's dataset via a shared URL; dataset is added to user's current history."""
# Set referer message.
referer = trans.request.referer
if referer and not referer.startswith(f"{trans.request.application_url}{url_for('/login')}"):
referer_message = f"<a href='{escape(referer)}'>return to the previous page</a>"
else:
referer_message = f"<a href='{url_for('/')}'>go to Galaxy's start page</a>"
# Error checking.
if not dataset_id:
return trans.show_error_message(
f"You must specify a dataset to import. You can {referer_message}.", use_panels=True
)
# Do import.
cur_history = trans.get_history(create=True)
status, message = self._copy_datasets(trans, [dataset_id], [cur_history], imported=True)
message = (
f"Dataset imported. <br>You can <a href='{url_for('/')}'>start using the dataset</a> or {referer_message}."
)
return trans.show_message(message, type=status, use_panels=True)

@web.expose
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."""
Expand Down Expand Up @@ -512,34 +487,6 @@ def display_by_username_and_slug(self, trans, username, slug, filename=None, pre
first_chunk=first_chunk,
)

@web.expose
def annotate_async(self, trans, id, new_annotation=None, **kwargs):
# TODO:?? why is this an access check only?
decoded_id = self.decode_id(id)
dataset = self.hda_manager.get_accessible(decoded_id, trans.user)
dataset = self.hda_manager.error_if_uploading(dataset)
if not dataset:
web.httpexceptions.HTTPNotFound()
if dataset and new_annotation:
# Sanitize annotation before adding it.
new_annotation = sanitize_html(new_annotation)
self.add_item_annotation(trans.sa_session, trans.get_user(), dataset, new_annotation)
with transaction(trans.sa_session):
trans.sa_session.commit()
return new_annotation

@web.expose
def get_annotation_async(self, trans, id):
decoded_id = self.decode_id(id)
dataset = self.hda_manager.get_accessible(decoded_id, trans.user)
dataset = self.hda_manager.error_if_uploading(dataset)
if not dataset:
web.httpexceptions.HTTPNotFound()
annotation = self.get_item_annotation_str(trans.sa_session, trans.user, dataset)
if annotation and isinstance(annotation, str):
annotation = annotation.encode("ascii", "replace") # paste needs ascii here
return annotation

@web.expose
def display_at(self, trans, dataset_id, filename=None, **kwd):
"""Sets up a dataset permissions so it is viewable at an external site"""
Expand Down Expand Up @@ -723,177 +670,6 @@ def display_application(
"You do not have permission to view this dataset at an external display application."
)

def _delete(self, trans, dataset_id):
message = None
status = "done"
id = None
try:
id = self.decode_id(dataset_id)
hda = self.hda_manager.get_owned(id, trans.user, current_history=trans.history)
self.hda_manager.error_unless_mutable(hda.history)
hda.mark_deleted()
hda.clear_associated_files()
trans.log_event(f"Dataset id {str(id)} marked as deleted")
self.hda_manager.stop_creating_job(hda, flush=True)
except Exception:
msg = f"HDA deletion failed (encoded: {dataset_id}, decoded: {id})"
log.exception(msg)
trans.log_event(msg)
message = "Dataset deletion failed"
status = "error"
return (message, status)

def _undelete(self, trans, dataset_id):
message = None
status = "done"
id = None
try:
id = self.decode_id(dataset_id)
item = self.hda_manager.get_owned(id, trans.user, current_history=trans.history)
self.hda_manager.error_unless_mutable(item.history)
self.hda_manager.undelete(item)
trans.log_event(f"Dataset id {str(id)} has been undeleted")
except Exception:
msg = f"HDA undeletion failed (encoded: {dataset_id}, decoded: {id})"
log.exception(msg)
trans.log_event(msg)
message = "Dataset undeletion failed"
status = "error"
return (message, status)

def _unhide(self, trans, dataset_id):
try:
id = self.decode_id(dataset_id)
item = self.hda_manager.get_owned(id, trans.user, current_history=trans.history)
self.hda_manager.error_unless_mutable(item.history)
item.mark_unhidden()
with transaction(trans.sa_session):
trans.sa_session.commit()
trans.log_event(f"Dataset id {str(id)} has been unhidden")
return True
except Exception:
return False

def _purge(self, trans, dataset_id):
message = None
status = "done"
try:
id = self.decode_id(dataset_id)
user = trans.get_user()
hda = trans.sa_session.query(self.app.model.HistoryDatasetAssociation).get(id)
# Invalid HDA
assert hda, "Invalid history dataset ID"

# If the user is anonymous, make sure the HDA is owned by the current session.
if not user:
current_history_id = trans.galaxy_session.current_history_id
assert hda.history.id == current_history_id, "Data does not belong to current user"
# If the user is known, make sure the HDA is owned by the current user.
else:
assert hda.history.user == user, "Data does not belong to current user"

# Ensure HDA is deleted
hda.deleted = True
# HDA is purgeable
# Decrease disk usage first
hda.purge_usage_from_quota(user, hda.dataset.quota_source_info)
# Mark purged
hda.purged = True
trans.sa_session.add(hda)
trans.log_event(f"HDA id {hda.id} has been purged")
with transaction(trans.sa_session):
trans.sa_session.commit()
# Don't delete anything if there are active HDAs or any LDDAs, even if
# the LDDAs are deleted. Let the cleanup scripts get it in the latter
# case.
if hda.dataset.user_can_purge:
try:
hda.dataset.full_delete()
trans.log_event(f"Dataset id {hda.dataset.id} has been purged upon the purge of HDA id {hda.id}")
trans.sa_session.add(hda.dataset)
except Exception:
log.exception(f"Unable to purge dataset ({hda.dataset.id}) on purge of HDA ({hda.id}):")
with transaction(trans.sa_session):
trans.sa_session.commit()
except Exception:
msg = f"HDA purge failed (encoded: {dataset_id}, decoded: {id})"
log.exception(msg)
trans.log_event(msg)
message = "Dataset removal from disk failed"
status = "error"
return (message, status)

@web.expose
def delete(self, trans, dataset_id, filename, show_deleted_on_refresh=False):
message, status = self._delete(trans, dataset_id)
return trans.response.send_redirect(
web.url_for(
controller="root",
action="history",
show_deleted=show_deleted_on_refresh,
message=message,
status=status,
)
)

@web.expose
def delete_async(self, trans, dataset_id, filename):
message, status = self._delete(trans, dataset_id)
if status == "done":
return "OK"
else:
raise Exception(message)

@web.expose
def undelete(self, trans, dataset_id, filename):
message, status = self._undelete(trans, dataset_id)
return trans.response.send_redirect(
web.url_for(controller="root", action="history", show_deleted=True, message=message, status=status)
)

@web.expose
def undelete_async(self, trans, dataset_id, filename):
message, status = self._undelete(trans, dataset_id)
if status == "done":
return "OK"
else:
raise Exception(message)

@web.expose
def unhide(self, trans, dataset_id, filename):
if self._unhide(trans, dataset_id):
return trans.response.send_redirect(web.url_for(controller="root", action="history", show_hidden=True))
raise Exception("Error unhiding")

@web.expose
def purge(self, trans, dataset_id, filename, show_deleted_on_refresh=False):
if trans.app.config.allow_user_dataset_purge:
message, status = self._purge(trans, dataset_id)
else:
message = "Removal of datasets by users is not allowed in this Galaxy instance. Please contact your Galaxy administrator."
status = "error"
return trans.response.send_redirect(
web.url_for(
controller="root",
action="history",
show_deleted=show_deleted_on_refresh,
message=message,
status=status,
)
)

@web.expose
def purge_async(self, trans, dataset_id, filename):
if trans.app.config.allow_user_dataset_purge:
message, status = self._purge(trans, dataset_id)
else:
message = "Removal of datasets by users is not allowed in this Galaxy instance. Please contact your Galaxy administrator."
status = "error"
if status == "done":
return "OK"
else:
raise Exception(message)

@web.expose
def copy_datasets(
self,
Expand Down Expand Up @@ -1039,53 +815,3 @@ def copy_datasets(
error_msg=error_msg,
refresh_frames=refresh_frames,
)

def _copy_datasets(self, trans, dataset_ids, target_histories, imported=False):
"""Helper method for copying datasets."""
user = trans.get_user()
done_msg = error_msg = ""

invalid_datasets = 0
if not dataset_ids or not target_histories:
error_msg = "You must provide both source datasets and target histories."
else:
# User must own target histories to copy datasets to them.
for history in target_histories:
if user != history.user:
error_msg = (
error_msg
+ "You do not have permission to add datasets to %i requested histories. "
% (len(target_histories))
)
for dataset_id in dataset_ids:
decoded_id = self.decode_id(dataset_id)
data = self.hda_manager.get_accessible(decoded_id, trans.user)
data = self.hda_manager.error_if_uploading(data)

if data is None:
error_msg = f"{error_msg}You tried to copy a dataset that does not exist or that you do not have access to. "
invalid_datasets += 1
else:
for hist in target_histories:
dataset_copy = data.copy()
if imported:
dataset_copy.name = f"imported: {dataset_copy.name}"
hist.add_dataset(dataset_copy)
with transaction(trans.sa_session):
trans.sa_session.commit()
num_datasets_copied = len(dataset_ids) - invalid_datasets
done_msg = "%i dataset%s copied to %i histor%s." % (
num_datasets_copied,
iff(num_datasets_copied == 1, "", "s"),
len(target_histories),
iff(len(target_histories) == 1, "y", "ies"),
)
trans.sa_session.refresh(history)

if error_msg != "":
status = ERROR
message = error_msg
else:
status = SUCCESS
message = done_msg
return status, message
4 changes: 0 additions & 4 deletions templates/webapps/galaxy/dataset/display.mako
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Original file line number Diff line number Diff line change
Expand Up @@ -82,10 +82,6 @@
%if data.deleted:
<div class="errormessagelarge" id="deleted-data-message">
You are viewing a deleted dataset.
%if data.history and data.history.user == trans.get_user():
<br />
<a href="javascript:void(0)" role="button" onclick="$.ajax( {type: 'GET', cache: false, url: '${h.url_for( controller='dataset', action='undelete_async', dataset_id=trans.security.encode_id( data.id ) )}', dataType: 'text', contentType: 'text/html', success: function( data, textStatus, jqXHR ){ if (data == 'OK' ){ $( '#deleted-data-message' ).slideUp( 'slow' ) } else { alert( 'Undelete failed.' ) } }, error: function( data, textStatus, jqXHR ){ alert( 'Undelete failed.' ); } } );">Undelete</a>
%endif
</div>
%endif
</%def>
Expand Down
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